Systems and methods for determining a treatment course of action

ABSTRACT

The present disclosure relates to methods of determining a treatment course of action. In particular, the present disclosure relates to mutations in the gene encoding estrogen receptor and their association with responsiveness to estrogen therapies for cancer.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application claims priority to U.S. Provisional Patent Application Ser. No. 61/892,743, filed Oct. 18, 2013, and U.S. Provisional Patent Application Ser. No. 61/992,615, filed May 13, 2014, the disclosures of which are herein incorporated by reference in their entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under CA111275 and HG006508 awarded by the National Institutes of Health. The Government has certain rights in the invention.

FIELD OF THE INVENTION

The present disclosure relates to methods of determining a treatment course of action. In particular, the present disclosure relates to mutations in the gene encoding estrogen receptor and their association with responsiveness to estrogen therapies for cancer.

BACKGROUND OF THE INVENTION

Breast cancer is the second most common form of cancer among women in the U.S., and the second leading cause of cancer deaths among women. While the 1980s saw a sharp rise in the number of new cases of breast cancer, that number now appears to have stabilized. The drop in the death rate from breast cancer is probably due to the fact that more women are having mammograms. When detected early, the chances for successful treatment of breast cancer are much improved.

Breast cancer, which is highly treatable by surgery, radiation therapy, chemotherapy, and hormonal therapy, is most often curable when detected in early stages. Mammography is the most important screening modality for the early detection of breast cancer. Breast cancer is classified into a variety of sub-types, but only a few of these affect prognosis or selection of therapy. Patient management following initial suspicion of breast cancer generally includes confirmation of the diagnosis, evaluation of stage of disease, and selection of therapy. Diagnosis may be confirmed by aspiration cytology, core needle biopsy with a stereotactic or ultrasound technique for nonpalpable lesions, or incisional or excisional biopsy. At the time the tumor tissue is surgically removed, part of it is processed for determination of ER and PR levels.

Prognosis and selection of therapy are influenced by the age of the patient, stage of the disease, pathologic characteristics of the primary tumor including the presence of tumor necrosis, estrogen-receptor (ER) and progesterone-receptor (PR) levels in the tumor tissue, HER2 overexpression status and measures of proliferative capacity, as well as by menopausal status and general health. Overweight patients may have a poorer prognosis (Bastarrachea et al., Annals of Internal Medicine, 120: 18 [1994]). Prognosis may also vary by race, with blacks, and to a lesser extent Hispanics, having a poorer prognosis than whites (Elledge et al., Journal of the National Cancer Institute 86: 705 [1994]; Edwards et al., Journal of Clinical Oncology 16: 2693 [1998]).

The three major treatments for breast cancer are surgery, radiation, and drug therapy. No treatment fits every patient, and often two or more are required. The choice is determined by many factors, including the age of the patient and her menopausal status, the type of cancer (e.g., ductal vs. lobular), its stage, whether the tumor is hormone-receptive or not, and its level of invasiveness.

Breast cancer treatments are defined as local or systemic. Surgery and radiation are considered local therapies because they directly treat the tumor, breast, lymph nodes, or other specific regions. Drug treatment is called systemic therapy, because its effects are wide spread. Drug therapies include classic chemotherapy drugs, hormone blocking treatment (e.g., aromatase inhibitors, selective estrogen receptor modulators, and estrogen receptor downregulators), and monoclonal antibody treatment (e.g., against HER2). They may be used separately or, most often, in different combinations.

There is a need for additional diagnostic and treatment options, particularly treatments customized to a patient's tumor.

SUMMARY OF THE INVENTION

The present disclosure relates to methods of determining a treatment course of action. In particular, the present disclosure relates to mutations in the gene encoding estrogen receptor and their association with responsiveness to estrogen therapies for cancer. In some embodiments, the present disclosure provides a method of treating cancer, comprising: assaying a sample from a subject diagnosed with cancer for the presence of a mutation in the estrogen receptor (ESR1) gene (e.g. one or more of p.Leu536Gln, p.Tyr537Ser, p.Tyr537Cys, or p.Tyr537Asn); and determining a treatment course of action based on the presence of the mutation. In some embodiments, the method further comprises the step of administering the treatment when the mutation is present. In some embodiments, the treatment is an estrogen receptor antagonist (e.g., tamoxifen or fulvestrant). In some embodiments, the sample is, for example, tissue, blood, plasma, serum, endometrial cells, or breast cells. In some embodiments, the cancer is breast cancer or endometrial cancer. In some embodiments, the detecting comprises forming a complex between the ESR1 gene and a nucleic acid primer, probe, or pair of primers that specifically bind to the ESR1 gene. In some embodiments, the nucleic acid primer, probe, or pair of primers bind to the mutation in said ESR1 gene but not the wild type gene. In some embodiments, the ESR1 gene is assayed from circulating tumor nucleic acid. In some embodiments, the detecting comprising forming a complex between the mutant ESR1 polypeptide and an antibody that specifically binds to the variant amino acid sequence.

Further embodiments provide a method of monitoring treatment of cancer, comprising: administering a cancer therapy to a subject; assaying a sample from a subject diagnosed with cancer for the presence of a mutation in the estrogen receptor (ESR1) gene (e.g., p.Leu536Gln, p.Tyr537Ser, p.Tyr537Cys, or p.Tyr537Asn); and determining a treatment course of action based on the presence of the mutation. In some embodiments, the method further comprises the step of administering the treatment when the mutations are present. In some embodiments, the cancer therapy is an aromatase inhibitor.

Additional embodiments provide a complex comprising a nucleic acid encoding estrogen receptor (ESR1) gene comprising a mutation selected from, for example, p.Leu536Gln, p.Tyr537Ser, p.Tyr537Cys, or p.Tyr537Asn and a nucleic acid primer or probe that specifically hybridizes to a variant ESR1 nucleic acid endocing the mutant polypeptide but not the wild type nucleic acid. In some embodiments, a reaction mixture comprising a mutant ESR1 polypeptide and an antibody that specifically binds to the variant amino acid sequence is provided. In some embodiments, the present invention provides a multiplex (e.g., microarray) comprising reagents that binds to two or more variant ESR1 amino acid or nucleic acids.

In some embodiments, the present invention provides one or more nucleic acid probes or primers having 8 or more (e.g., 10 or more, 12 or more, 15 or more, 18 or more, etc.) nucleotides and that specifically bind to nucleic acids encoding a variant ESR polypeptide but not the wild type nucleic acid. In some embodiments, the present invention provides an antibody that specifically binds to variant ESR1 polypeptides but not wild type ESR1 polypeptides.

In some embodiments, the present invention provides a system comprising a computer processor and computer software configured to analyze information on the presence and absence of variant ESR1 polypeptides or amino acids encoding the polypeptides; and determine a treatment course of action based on the presence or absence of the variant gene or polypeptide.

Additional embodiments are described herein.

DESCRIPTION OF THE FIGURES

FIG. 1 shows clinical timelines of the six index ER-positive metastatic breast cancer patients harboring ESR1 mutations.

FIG. 2 shows a schematic representation of ESR1 mutations identified in the experiments described herein.

FIG. 3 shows that acquired ESR1 mutations are constitutively active.

FIG. 4 shows that acquired ESR1 mutations maintain sensitivity to antiestrogen therapies. Steroid hormone-deprived cells were either untreated or treated with increasing doses of antiestrogen drugs tamoxifen (A) or fulvestrant (B) in the presence of 5 nM of β-estradiol (E2) for 24 hrs.

FIG. 5 shows that gene copy number landscape of the six index cases as assessed by whole exome sequencing matched to germline.

FIG. 6 shows schematic representations of the predicted gene fusions identified by transcriptome sequencing in four breast cancer index cases. a, MO_(—)1031: PLA2G12A-COL15A1. b, MO_(—)1031: IPO9-PM20D1. c, MO_(—)1031: LRP5-FAT3. d, MO_(—)1051:CMASPIK3C2G. e, MO_(—)1051: TBCK-PPA2. f, MO_(—)1051: GPATCH8-MPP2. g, MO_(—)1051: FGFR2-AFF3. h, MO_(—)1069: UBN2-TTC26. i, MO_(—)1069: TBCD-FOXK2. j, MO_(—)1129: DDB1-PAK1. k, MO_(—)1129: VPS35-SLCO2B1.

FIG. 7 shows an analysis of transactivational activity of wild type and mutant ESR1 variants by luciferase reporter assay.

FIG. 8 shows dose response of the wild type and mutant ESR1 variants to 4-hydroxytamoxifen, in competition with 1 nM estradiol.

FIG. 9 shows dose response of the wild type and mutant ESR1 variants to fulvestrant, in competition with 1 nM estradiol.

FIG. 10 shows inhibition of transactivation activity of wild type and mutant ESR1 variants by endoxifen.

FIG. 11 shows dose response of the wild type and mutant ESR1 variants to estradiol.

DEFINITIONS

To facilitate an understanding of the present invention, a number of terms and phrases are defined below:

As used herein, the terms “detect”, “detecting” or “detection” may describe either the general act of discovering or discerning or the specific observation of a detectably labeled composition.

As used herein, the term “subject” refers to any organisms that are screened using the diagnostic methods described herein. Such organisms preferably include, but are not limited to, mammals (e.g., humans).

The term “diagnosed,” as used herein, refers to the recognition of a disease by its signs and symptoms, or genetic analysis, pathological analysis, histological analysis, and the like.

As used herein, the term “characterizing cancer in a subject” refers to the identification of one or more properties of a cancer sample in a subject, including but not limited to, the presence of benign, pre-cancerous or cancerous tissue, the stage of the cancer, and the subject's prognosis. Cancers may be characterized by the identification of the expression of one or more cancer marker genes, including but not limited to, the ESR1 variants disclosed herein.

As used herein, the term “characterizing cancer in a subject” refers to the identification of one or more properties of a cancer sample (e.g., including but not limited to, the presence of cancerous tissue, the presence or absence of ESR1 mutation, the presence of pre-cancerous tissue that is likely to become cancerous, and the presence of cancerous tissue that is likely to metastasize). In some embodiments, tissues are characterized by the identification of the expression of one or more cancer marker genes, including but not limited to, the cancer markers disclosed herein.

As used herein, the term “stage of cancer” refers to a qualitative or quantitative assessment of the level of advancement of a cancer. Criteria used to determine the stage of a cancer include, but are not limited to, the size of the tumor and the extent of metastases (e.g., localized or distant).

As used herein, the term “nucleic acid molecule” refers to any nucleic acid containing molecule, including but not limited to, DNA or RNA. The term encompasses sequences that include any of the known base analogs of DNA and RNA including, but not limited to, 4-acetylcytosine, 8-hydroxy-N6-methyladenosine, aziridinylcytosine, pseudoisocytosine, 5-(carboxyhydroxylmethyl) uracil, 5-fluorouracil, 5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil, 5-carboxymethylaminomethyluracil, dihydrouracil, inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-methyladenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxy-aminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarbonylmethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, N-uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and 2,6-diaminopurine.

The term “gene” refers to a nucleic acid (e.g., DNA) sequence that comprises coding sequences necessary for the production of a polypeptide, precursor, or RNA (e.g., rRNA, tRNA). The polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or functional properties (e.g., enzymatic activity, ligand binding, signal transduction, immunogenicity, etc.) of the full-length or fragments are retained. The term also encompasses the coding region of a structural gene and the sequences located adjacent to the coding region on both the 5′ and 3′ ends for a distance of about 1 kb or more on either end such that the gene corresponds to the length of the full-length mRNA. Sequences located 5′ of the coding region and present on the mRNA are referred to as 5′ non-translated sequences. Sequences located 3′ or downstream of the coding region and present on the mRNA are referred to as 3′ non-translated sequences. The term “gene” encompasses both cDNA and genomic forms of a gene. A genomic form or clone of a gene contains the coding region interrupted with non-coding sequences termed “introns” or “intervening regions” or “intervening sequences.” Introns are segments of a gene that are transcribed into nuclear RNA (hnRNA); introns may contain regulatory elements such as enhancers. Introns are removed or “spliced out” from the nuclear or primary transcript; introns therefore are absent in the messenger RNA (mRNA) transcript. The mRNA functions during translation to specify the sequence or order of amino acids in a nascent polypeptide.

As used herein, the term “oligonucleotide,” refers to a short length of single-stranded polynucleotide chain. Oligonucleotides are typically less than 200 residues long (e.g., between 15 and 100), however, as used herein, the term is also intended to encompass longer polynucleotide chains. Oligonucleotides are often referred to by their length. For example a 24 residue oligonucleotide is referred to as a “24-mer”. Oligonucleotides can form secondary and tertiary structures by self-hybridizing or by hybridizing to other polynucleotides. Such structures can include, but are not limited to, duplexes, hairpins, cruciforms, bends, and triplexes.

As used herein, the terms “complementary” or “complementarity” are used in reference to polynucleotides (i.e., a sequence of nucleotides) related by the base-pairing rules. For example, the sequence “5′-A-G-T-3′,” is complementary to the sequence “3′-T-C-A-5′.” Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands. This is of particular importance in amplification reactions, as well as detection methods that depend upon binding between nucleic acids.

The term “homology” refers to a degree of complementarity. There may be partial homology or complete homology (i.e., identity). A partially complementary sequence is a nucleic acid molecule that at least partially inhibits a completely complementary nucleic acid molecule from hybridizing to a target nucleic acid is “substantially homologous.” The inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or Northern blot, solution hybridization and the like) under conditions of low stringency. A substantially homologous sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely homologous nucleic acid molecule to a target under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction. The absence of non-specific binding may be tested by the use of a second target that is substantially non-complementary (e.g., less than about 30% identity); in the absence of non-specific binding the probe will not hybridize to the second non-complementary target.

As used herein, the term “hybridization” is used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acids) is impacted by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, the T_(m) of the formed hybrid, and the G:C ratio within the nucleic acids. A single molecule that contains pairing of complementary nucleic acids within its structure is said to be “self-hybridized.”

As used herein the term “stringency” is used in reference to the conditions of temperature, ionic strength, and the presence of other compounds such as organic solvents, under which nucleic acid hybridizations are conducted. Under “low stringency conditions” a nucleic acid sequence of interest will hybridize to its exact complement, sequences with single base mismatches, closely related sequences (e.g., sequences with 90% or greater homology), and sequences having only partial homology (e.g., sequences with 50-90% homology). Under ‘medium stringency conditions,” a nucleic acid sequence of interest will hybridize only to its exact complement, sequences with single base mismatches, and closely relation sequences (e.g., 90% or greater homology). Under “high stringency conditions,” a nucleic acid sequence of interest will hybridize only to its exact complement, and (depending on conditions such a temperature) sequences with single base mismatches. In other words, under conditions of high stringency the temperature can be raised so as to exclude hybridization to sequences with single base mismatches.

The term “isolated” when used in relation to a nucleic acid, as in “an isolated oligonucleotide” or “isolated polynucleotide” refers to a nucleic acid sequence that is identified and separated from at least one component or contaminant with which it is ordinarily associated in its natural source. Isolated nucleic acid is such present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated nucleic acids as nucleic acids such as DNA and RNA found in the state they exist in nature. For example, a given DNA sequence (e.g., a gene) is found on the host cell chromosome in proximity to neighboring genes; RNA sequences, such as a specific mRNA sequence encoding a specific protein, are found in the cell as a mixture with numerous other mRNAs that encode a multitude of proteins. However, isolated nucleic acid encoding a given protein includes, by way of example, such nucleic acid in cells ordinarily expressing the given protein where the nucleic acid is in a chromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature. The isolated nucleic acid, oligonucleotide, or polynucleotide may be present in single-stranded or double-stranded form. When an isolated nucleic acid, oligonucleotide or polynucleotide is to be utilized to express a protein, the oligonucleotide or polynucleotide will contain at a minimum the sense or coding strand (i.e., the oligonucleotide or polynucleotide may be single-stranded), but may contain both the sense and anti-sense strands (i.e., the oligonucleotide or polynucleotide may be double-stranded).

As used herein, the term “purified” or “to purify” refers to the removal of components (e.g., contaminants) from a sample. For example, antibodies are purified by removal of contaminating non-immunoglobulin proteins; they are also purified by the removal of immunoglobulin that does not bind to the target molecule. The removal of non-immunoglobulin proteins and/or the removal of immunoglobulins that do not bind to the target molecule results in an increase in the percent of target-reactive immunoglobulins in the sample. In another example, recombinant polypeptides are expressed in bacterial host cells and the polypeptides are purified by the removal of host cell proteins; the percent of recombinant polypeptides is thereby increased in the sample.

As used herein, the term “sample” is used in its broadest sense. In one sense, it is meant to include a specimen or culture obtained from any source, as well as biological and environmental samples. Biological samples may be obtained from animals (including humans) and encompass fluids, solids, tissues (e.g., biopsy samples), cells, and gases. Biological samples include blood products, such as plasma, serum and the like. Such examples are not however to be construed as limiting the sample types applicable to the present invention.

DETAILED DESCRIPTION OF THE INVENTION

The present disclosure relates to methods of determining a treatment course of action. In particular, the present disclosure relates to mutations in the gene encoding estrogen receptor and their association with responsiveness to estrogen therapies for cancer.

I. Diagnostic and Screening Methods

As described above, embodiments of the present invention provide diagnostic and screening methods that utilize the detection of mutations in ligand binding region of the estrogen receptor (ESR1) gene (e.g., p.Leu536Gln, p.Tyr537Ser, p.Tyr537Cys, p.Tyr537Asn, and p.Asp538Gly). Exemplary, non-limiting methods are described below.

Any patient sample suspected of containing the ESR1 gene may be tested according to methods of embodiments of the present invention. By way of non-limiting examples, the sample may be tissue (e.g., a breast, endometrial, ovarian, or uterine biopsy sample), blood, urine, or a fraction thereof (e.g., plasma, serum, cells).

In some embodiments, the patient sample is subjected to preliminary processing designed to isolate or enrich the sample for the ESR1 gens or cells that contain the gene. A variety of techniques known to those of ordinary skill in the art may be used for this purpose, including but not limited to: centrifugation; immunocapture; cell lysis; and, nucleic acid target capture (See, e.g., EP Pat. No. 1 409 727, herein incorporated by reference in its entirety).

In some embodiments, mutations in the ESR1 gene are monitored in circulating tumor DNA (See e.g., Dawson, S. J. et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 368, 1199-209 (2013); Diehl, F. et al. Nat Med 14, 985-90 (2008)).

In some embodiments, the ESR1 mutations are detected along with other markers in a multiplex or panel format. Markers are selected for their predictive value alone or in combination with the ESR1 mutations. Markers for other cancers, diseases, infections, and metabolic conditions are also contemplated for inclusion in a multiplex or panel format.

i. DNA and RNA Detection

The ESR1 mutation are detected using a variety of nucleic acid techniques known to those of ordinary skill in the art, including but not limited to: nucleic acid sequencing; nucleic acid hybridization; and, nucleic acid amplification.

1. Sequencing

A variety of nucleic acid sequencing methods are contemplated for use in the methods of the present disclosure including, for example, chain terminator (Sanger) sequencing, dye terminator sequencing, and high-throughput sequencing methods. Many of these sequencing methods are well known in the art. See, e.g., Sanger et al., Proc. Natl. Acad. Sci. USA 74:5463-5467 (1997); Maxam et al., Proc. Natl. Acad. Sci. USA 74:560-564 (1977); Drmanac, et al., Nat. Biotechnol. 16:54-58 (1998); Kato, Int. J. Clin. Exp. Med. 2:193-202 (2009); Ronaghi et al., Anal. Biochem. 242:84-89 (1996); Margulies et al., Nature 437:376-380 (2005); Ruparel et al., Proc. Natl. Acad. Sci. USA 102:5932-5937 (2005), and Harris et al., Science 320:106-109 (2008); Levene et al., Science 299:682-686 (2003); Korlach et al., Proc. Natl. Acad. Sci. USA 105:1176-1181 (2008); Branton et al., Nat. Biotechnol. 26(10):1146-53 (2008); Eid et al., Science 323:133-138 (2009); each of which is herein incorporated by reference in its entirety.

Next-generation sequencing (NGS) methods share the common feature of massively parallel, high-throughput strategies, with the goal of lower costs in comparison to older sequencing methods (see, e.g., Voelkerding et al., Clinical Chem., 55: 641-658, 2009; MacLean et al., Nature Rev. Microbiol., 7: 287-296; each herein incorporated by reference in their entirety). NGS methods can be broadly divided into those that typically use template amplification and those that do not. Amplification-requiring methods include pyrosequencing commercialized by Roche as the 454 technology platforms (e.g., GS 20 and GS FLX), the Solexa platform commercialized by Illumina, and the Supported Oligonucleotide Ligation and Detection (SOLiD) platform commercialized by Applied Biosystems. Non-amplification approaches, also known as single-molecule sequencing, are exemplified by the HeliScope platform commercialized by Helicos BioSciences, and emerging platforms commercialized by VisiGen, Oxford Nanopore Technologies Ltd., Life Technologies/Ion Torrent, and Pacific Biosciences, respectively.

In pyrosequencing (Voelkerding et al., Clinical Chem., 55: 641-658, 2009; MacLean et al., Nature Rev. Microbiol., 7: 287-296; U.S. Pat. No. 6,210,891; U.S. Pat. No. 6,258,568; each herein incorporated by reference in its entirety), template DNA is fragmented, end-repaired, ligated to adaptors, and clonally amplified in-situ by capturing single template molecules with beads bearing oligonucleotides complementary to the adaptors. Each bead bearing a single template type is compartmentalized into a water-in-oil microvesicle, and the template is clonally amplified using a technique referred to as emulsion PCR. The emulsion is disrupted after amplification and beads are deposited into individual wells of a picotitre plate functioning as a flow cell during the sequencing reactions. Ordered, iterative introduction of each of the four dNTP reagents occurs in the flow cell in the presence of sequencing enzymes and luminescent reporter such as luciferase. In the event that an appropriate dNTP is added to the 3′ end of the sequencing primer, the resulting production of ATP causes a burst of luminescence within the well, which is recorded using a CCD camera. It is possible to achieve read lengths greater than or equal to 400 bases, and 10⁶ sequence reads can be achieved, resulting in up to 500 million base pairs (Mb) of sequence.

In the Solexa/Illumina platform (Voelkerding et al., Clinical Chem., 55: 641-658, 2009; MacLean et al., Nature Rev. Microbiol., 7: 287-296; U.S. Pat. No. 6,833,246; U.S. Pat. No. 7,115,400; U.S. Pat. No. 6,969,488; each herein incorporated by reference in its entirety), sequencing data are produced in the form of shorter-length reads. In this method, single-stranded fragmented DNA is end-repaired to generate 5′-phosphorylated blunt ends, followed by Klenow-mediated addition of a single A base to the 3′ end of the fragments. A-addition facilitates addition of T-overhang adaptor oligonucleotides, which are subsequently used to capture the template-adaptor molecules on the surface of a flow cell that is studded with oligonucleotide anchors. The anchor is used as a PCR primer, but because of the length of the template and its proximity to other nearby anchor oligonucleotides, extension by PCR results in the “arching over” of the molecule to hybridize with an adjacent anchor oligonucleotide to form a bridge structure on the surface of the flow cell. These loops of DNA are denatured and cleaved. Forward strands are then sequenced with reversible dye terminators. The sequence of incorporated nucleotides is determined by detection of post-incorporation fluorescence, with each fluor and block removed prior to the next cycle of dNTP addition. Sequence read length ranges from 36 nucleotides to over 250 nucleotides, with overall output exceeding 1 billion nucleotide pairs per analytical run.

Sequencing nucleic acid molecules using SOLiD technology (Voelkerding et al., Clinical Chem., 55: 641-658, 2009; MacLean et al., Nature Rev. Microbiol., 7: 287-296; U.S. Pat. No. 5,912,148; U.S. Pat. No. 6,130,073; each herein incorporated by reference in their entirety) also involves fragmentation of the template, ligation to oligonucleotide adaptors, attachment to beads, and clonal amplification by emulsion PCR. Following this, beads bearing template are immobilized on a derivatized surface of a glass flow-cell, and a primer complementary to the adaptor oligonucleotide is annealed. However, rather than utilizing this primer for 3′ extension, it is instead used to provide a 5′ phosphate group for ligation to interrogation probes containing two probe-specific bases followed by 6 degenerate bases and one of four fluorescent labels. In the SOLiD system, interrogation probes have 16 possible combinations of the two bases at the 3′ end of each probe, and one of four fluors at the 5′ end. Fluor color, and thus identity of each probe, corresponds to specified color-space coding schemes. Multiple rounds (usually 7) of probe annealing, ligation, and fluor detection are followed by denaturation, and then a second round of sequencing using a primer that is offset by one base relative to the initial primer. In this manner, the template sequence can be computationally re-constructed, and template bases are interrogated twice, resulting in increased accuracy. Sequence read length averages 35 nucleotides, and overall output exceeds 4 billion bases per sequencing run.

In certain embodiments, nanopore sequencing (see, e.g., Astier et al., J. Am. Chem. Soc. 2006 Feb. 8; 128(5):1705-10, herein incorporated by reference) is utilized. The theory behind nanopore sequencing has to do with what occurs when a nanopore is immersed in a conducting fluid and a potential (voltage) is applied across it. Under these conditions a slight electric current due to conduction of ions through the nanopore can be observed, and the amount of current is exceedingly sensitive to the size of the nanopore. As each base of a nucleic acid passes through the nanopore, this causes a change in the magnitude of the current through the nanopore that is distinct for each of the four bases, thereby allowing the sequence of the DNA molecule to be determined.

In certain embodiments, HeliScope by Helicos BioSciences (Voelkerding et al., Clinical Chem., 55: 641-658, 2009; MacLean et al., Nature Rev. Microbiol., 7: 287-296; U.S. Pat. No. 7,169,560; U.S. Pat. No. 7,282,337; U.S. Pat. No. 7,482,120; U.S. Pat. No. 7,501,245; U.S. Pat. No. 6,818,395; U.S. Pat. No. 6,911,345; U.S. Pat. No. 7,501,245; each herein incorporated by reference in their entirety) is utilized. Template DNA is fragmented and polyadenylated at the 3′ end, with the final adenosine bearing a fluorescent label. Denatured polyadenylated template fragments are ligated to poly(dT) oligonucleotides on the surface of a flow cell. Initial physical locations of captured template molecules are recorded by a CCD camera, and then label is cleaved and washed away. Sequencing is achieved by addition of polymerase and serial addition of fluorescently-labeled dNTP reagents. Incorporation events result in fluor signal corresponding to the dNTP, and signal is captured by a CCD camera before each round of dNTP addition. Sequence read length ranges from 25-50 nucleotides, with overall output exceeding 1 billion nucleotide pairs per analytical run.

The Ion Torrent technology is a method of DNA sequencing based on the detection of hydrogen ions that are released during the polymerization of DNA (see, e.g., Science 327(5970): 1190 (2010); U.S. Pat. Appl. Pub. Nos. 20090026082, 20090127589, 20100301398, 20100197507, 20100188073, and 20100137143, incorporated by reference in their entireties for all purposes). A microwell contains a template DNA strand to be sequenced. Beneath the layer of microwells is a hypersensitive ISFET ion sensor. All layers are contained within a CMOS semiconductor chip, similar to that used in the electronics industry. When a dNTP is incorporated into the growing complementary strand a hydrogen ion is released, which triggers a hypersensitive ion sensor. If homopolymer repeats are present in the template sequence, multiple dNTP molecules will be incorporated in a single cycle. This leads to a corresponding number of released hydrogens and a proportionally higher electronic signal. This technology differs from other sequencing technologies in that no modified nucleotides or optics are used. The per-base accuracy of the Ion Torrent sequencer is ˜99.6% for 50 base reads, with ˜100 Mb to 100 Gb generated per run. The read-length is 100-300 base pairs. The accuracy for homopolymer repeats of 5 repeats in length is ˜98%. The benefits of ion semiconductor sequencing are rapid sequencing speed and low upfront and operating costs.

Stratos Genomics, Inc. sequencing involves the use of Xpandomers. This sequencing process typically includes providing a daughter strand produced by a template-directed synthesis. The daughter strand generally includes a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of a target nucleic acid in which the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand. The Xpandomer typically includes the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected. Additional details relating to Xpandomer-based approaches are described in, for example, U.S. Pat. Pub No. 20090035777, entitled “High Throughput Nucleic Acid Sequencing by Expansion,” filed Jun. 19, 2008, which is incorporated herein in its entirety.

Other emerging single molecule sequencing methods include real-time sequencing by synthesis using a VisiGen platform (Voelkerding et al., Clinical Chem., 55: 641-58, 2009; U.S. Pat. No. 7,329,492; U.S. patent application Ser. No. 11/671,956; U.S. patent application Ser. No. 11/781,166; each herein incorporated by reference in their entirety) in which immobilized, primed DNA template is subjected to strand extension using a fluorescently-modified polymerase and florescent acceptor molecules, resulting in detectible fluorescence resonance energy transfer (FRET) upon nucleotide addition.

2. Hybridization

Illustrative non-limiting examples of nucleic acid hybridization techniques include, but are not limited to, in situ hybridization (ISH), microarray, and Southern or Northern blot. In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA or RNA strand as a probe to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough, the entire tissue (whole mount ISH). DNA ISH can be used to determine the structure of chromosomes. RNA ISH is used to measure and localize mRNAs and other transcripts within tissue sections or whole mounts. Sample cells and tissues are usually treated to fix the target transcripts in place and to increase access of the probe. The probe hybridizes to the target sequence at elevated temperature, and then the excess probe is washed away. The probe that was labeled with either radio-, fluorescent- or antigen-labeled bases is localized and quantitated in the tissue using either autoradiography, fluorescence microscopy or immunohistochemistry, respectively. ISH can also use two or more probes, labeled with radioactivity or the other non-radioactive labels, to simultaneously detect two or more transcripts.

In some embodiments, ESR1 mutations are detected using fluorescence in situ hybridization (FISH). In some embodiments, FISH assays utilize bacterial artificial chromosomes (BACs). These have been used extensively in the human genome sequencing project (see Nature 409: 953-958 (2001)) and clones containing specific BACs are available through distributors that can be located through many sources, e.g., NCBI. Each BAC clone from the human genome has been given a reference name that unambiguously identifies it. These names can be used to find a corresponding GenBank sequence and to order copies of the clone from a distributor.

The present invention further provides a method of performing a FISH assay on human cells (e.g., breast or endometrial cells). Specific protocols are well known in the art and can be readily adapted for the present invention. Guidance regarding methodology may be obtained from many references including: In situ Hybridization: Medical Applications (eds. G. R. Coulton and J. de Belleroche), Kluwer Academic Publishers, Boston (1992); In situ Hybridization: In Neurobiology; Advances in Methodology (eds. J. H. Eberwine, K. L. Valentino, and J. D. Barchas), Oxford University Press Inc., England (1994); In situ Hybridization: A Practical Approach (ed. D. G. Wilkinson), Oxford University Press Inc., England (1992)); Kuo, et al., Am. J. Hum. Genet. 49:112-119 (1991); Klinger, et al., Am. J. Hum. Genet. 51:55-65 (1992); and Ward, et al., Am. J. Hum. Genet. 52:854-865 (1993)). There are also kits that are commercially available and that provide protocols for performing FISH assays (available from e.g., Oncor, Inc., Gaithersburg, Md.). Patents providing guidance on methodology include U.S. Pat. Nos. 5,225,326; 5,545,524; 6,121,489 and 6,573,043. All of these references are hereby incorporated by reference in their entirety and may be used along with similar references in the art and with the information provided in the Examples section herein to establish procedural steps convenient for a particular laboratory.

3. Microarrays

Different kinds of biological assays are called microarrays including, but not limited to: DNA microarrays (e.g., cDNA microarrays and oligonucleotide microarrays); protein microarrays; tissue microarrays; transfection or cell microarrays; chemical compound microarrays; and, antibody microarrays. A DNA microarray, commonly known as gene chip, DNA chip, or biochip, is a collection of microscopic DNA spots attached to a solid surface (e.g., glass, plastic or silicon chip) forming an array for the purpose of expression profiling or monitoring expression levels for thousands of genes simultaneously. The affixed DNA segments are known as probes, thousands of which can be used in a single DNA microarray. Microarrays can be used to identify disease genes or transcripts (e.g., ESR1 mutations) by comparing gene expression in disease and normal cells. Microarrays can be fabricated using a variety of technologies, including but not limiting: printing with fine-pointed pins onto glass slides; photolithography using pre-made masks; photolithography using dynamic micromirror devices; ink jet printing; or, electrochemistry on microelectrode arrays.

Southern and Northern blotting is used to detect specific DNA or RNA sequences, respectively. DNA or RNA extracted from a sample is fragmented, electrophoretically separated on a matrix gel, and transferred to a membrane filter. The filter bound DNA or RNA is subject to hybridization with a labeled probe complementary to the sequence of interest. Hybridized probe bound to the filter is detected. A variant of the procedure is the reverse Northern blot, in which the substrate nucleic acid that is affixed to the membrane is a collection of isolated DNA fragments and the probe is RNA extracted from a tissue and labeled.

4. Amplification

Nucleic acids may be amplified prior to or simultaneous with detection. Illustrative non-limiting examples of nucleic acid amplification techniques include, but are not limited to, polymerase chain reaction (PCR), reverse transcription polymerase chain reaction (RT-PCR), transcription-mediated amplification (TMA), ligase chain reaction (LCR), strand displacement amplification (SDA), and nucleic acid sequence based amplification (NASBA). Those of ordinary skill in the art will recognize that certain amplification techniques (e.g., PCR) require that RNA be reversed transcribed to DNA prior to amplification (e.g., RT-PCR), whereas other amplification techniques directly amplify RNA (e.g., TMA and NASBA).

5. Protein Detection

In some embodiments, variant ESR1 polypeptides are detected (e.g., using immunoassays or mass spectrometry).

Illustrative non-limiting examples of immunoassays include, but are not limited to: immunoprecipitation; Western blot; ELISA; immunohistochemistry; immunocytochemistry; flow cytometry; and, immuno-PCR. Polyclonal or monoclonal antibodies detectably labeled using various techniques known to those of ordinary skill in the art (e.g., colorimetric, fluorescent, chemiluminescent or radioactive) are suitable for use in the immunoassays. Immunoprecipitation is the technique of precipitating an antigen out of solution using an antibody specific to that antigen. The process can be used to identify protein complexes present in cell extracts by targeting a protein believed to be in the complex. The complexes are brought out of solution by insoluble antibody-binding proteins isolated initially from bacteria, such as Protein A and Protein G. The antibodies can also be coupled to sepharose beads that can easily be isolated out of solution. After washing, the precipitate can be analyzed using mass spectrometry, Western blotting, or any number of other methods for identifying constituents in the complex.

A Western blot, or immunoblot, is a method to detect protein in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate denatured proteins by mass. The proteins are then transferred out of the gel and onto a membrane, typically polyvinyldiflroride or nitrocellulose, where they are probed using antibodies specific to the protein of interest. As a result, researchers can examine the amount of protein in a given sample and compare levels between several groups.

An ELISA, short for Enzyme-Linked ImmunoSorbent Assay, is a biochemical technique to detect the presence of an antibody or an antigen in a sample. It utilizes a minimum of two antibodies, one of which is specific to the antigen and the other of which is coupled to an enzyme. The second antibody will cause a chromogenic or fluorogenic substrate to produce a signal. Variations of ELISA include sandwich ELISA, competitive ELISA, and ELISPOT. Because the ELISA can be performed to evaluate either the presence of antigen or the presence of antibody in a sample, it is a useful tool both for determining serum antibody concentrations and also for detecting the presence of antigen.

Immuno-polymerase chain reaction (IPCR) utilizes nucleic acid amplification techniques to increase signal generation in antibody-based immunoassays. Because no protein equivalence of PCR exists, that is, proteins cannot be replicated in the same manner that nucleic acid is replicated during PCR, the only way to increase detection sensitivity is by signal amplification. The target proteins are bound to antibodies which are directly or indirectly conjugated to oligonucleotides. Unbound antibodies are washed away and the remaining bound antibodies have their oligonucleotides amplified. Protein detection occurs via detection of amplified oligonucleotides using standard nucleic acid detection methods, including real-time methods.

Mass spectrometry has proven to be a valuable tool for the determination of molecular structures of molecules of many kinds, including biomolecules, and is widely practiced today. Purified proteins are digested with specific proteases (e.g. trypsin) and evaluated using mass spectrometry. Many alternative methods can also be used. For instance, either matrix-assisted laser desorption/ionization (MALDI) or electrospray ionization (ESI) mass spectrometric methods can be used. Furthermore, mass spectroscopy can be coupled with the use of two-dimensional gel electrophoretic separation of cellular proteins as an alternative to comprehensive pre-purification. Mass spectrometry can also be coupled with the use of peptide fingerprint database and various searching algorithms. Differences in post-translational modification, such as phosphorylation or glycosylation, can also be probed by coupling mass spectrometry with the use of various pretreatments such as with glycosylases and phosphatases. All of these methods are to be considered as part of this application.

In some embodiments, electrospray ionisation quadrupole mass spectrometry is utilized to detect ESR1 variants (See e.g., U.S. Pat. No. 8,658,396; herein incorporated by reference in its entirety).

6. Data Analysis

In some embodiments, a computer-based analysis program is used to translate the raw data generated by the detection assay (e.g., the presence, absence, or amount of a given marker or markers) into data of predictive value for a clinician. The clinician can access the predictive data using any suitable means. Thus, in some preferred embodiments, the present invention provides the further benefit that the clinician, who is not likely to be trained in genetics or molecular biology, need not understand the raw data. The data is presented directly to the clinician in its most useful form. The clinician is then able to immediately utilize the information in order to optimize the care of the subject.

The present invention contemplates any method capable of receiving, processing, and transmitting the information to and from laboratories conducting the assays, information provides, medical personal, and subjects. For example, in some embodiments of the present invention, a sample (e.g., a biopsy or a serum sample) is obtained from a subject and submitted to a profiling service (e.g., clinical lab at a medical facility, genomic profiling business, etc.), located in any part of the world (e.g., in a country different than the country where the subject resides or where the information is ultimately used) to generate raw data. Where the sample comprises a tissue or other biological sample, the subject may visit a medical center to have the sample obtained and sent to the profiling center, or subjects may collect the sample themselves (e.g., a urine sample) and directly send it to a profiling center. Where the sample comprises previously determined biological information, the information may be directly sent to the profiling service by the subject (e.g., an information card containing the information may be scanned by a computer and the data transmitted to a computer of the profiling center using an electronic communication systems). Once received by the profiling service, the sample is processed and a profile is produced (i.e., ESR1 variant data), specific for the diagnostic or prognostic information desired for the subject.

The profile data is then prepared in a format suitable for interpretation by a treating clinician. For example, rather than providing raw expression data, the prepared format may represent a diagnosis or risk assessment (e.g., presence or absence of a mutation in ESR1) for the subject, along with recommendations for particular treatment options. The data may be displayed to the clinician by any suitable method. For example, in some embodiments, the profiling service generates a report that can be printed for the clinician (e.g., at the point of care) or displayed to the clinician on a computer monitor.

In some embodiments, the information is first analyzed at the point of care or at a regional facility. The raw data is then sent to a central processing facility for further analysis and/or to convert the raw data to information useful for a clinician or patient. The central processing facility provides the advantage of privacy (all data is stored in a central facility with uniform security protocols), speed, and uniformity of data analysis. The central processing facility can then control the fate of the data following treatment of the subject. For example, using an electronic communication system, the central facility can provide data to the clinician, the subject, or researchers.

In some embodiments, the subject is able to directly access the data using the electronic communication system. The subject may chose further intervention or counseling based on the results. In some embodiments, the data is used for research use. For example, the data may be used to further optimize the inclusion or elimination of markers as useful indicators of a particular condition or stage of disease or as a companion diagnostic to determine a treatment course of action.

6. Compositions & Kits

Compositions for use in the diagnostic methods described herein include, but are not limited to, probes, amplification oligonucleotides, and the like. In some embodiments, kits include all components necessary, sufficient or useful for detecting the markers described herein (e.g., reagents, controls, instructions, etc.). The kits described herein find use in research, therapeutic, screening, and clinical applications.

The probe and antibody compositions of the present invention may also be provided in the form of an array.

In some embodiments, the present invention provides one or more nucleic acid probes or primers having 8 or more (e.g., 10 or more, 12 or more, 15 or more, 18 or more, etc.) nucleotides, and that specifically bind to nucleic acids encoding a variant ESR polypeptide but not the wild type nucleic acid. In some embodiments, the present invention provides an antibody that specifically binds to variant ESR1 polypeptides but not wild type ESR1 polypeptides.

Embodiments of the present invention provide complexes of ESR1 nucleic acids or polypeptides with nucleic acid primers or probes or antibodies. In some embodiments, the primers, probes, or antibodies bind only to the variant or mutant forms of ESR1 described herein. In some embodiments, a reaction mixture comprising a mutant ESR1 polypeptide and an antibody that specifically binds to the variant amino acid sequence is provided. In some embodiments, the present invention provides a multiplex (e.g., microarray) comprising reagents that binds to two or more variant ESR1 amino acid or nucleic acids.

III. Treatment Methods

Embodiments of the present disclosure provide methods of determining a treatment course of action and administering an anti-cancer treatment. For example, in some embodiments, subjects diagnosed with cancer (e.g., endometrial cancer or breast cancer) are screened for the presence or absence of one or more of the ESR1 mutations described herein (e.g., p.Leu536Gln, p.Tyr537Ser, p.Tyr537Cys, or p.Tyr537Asn) and the results are used to determine a treatment course of action. For example, in some embodiments, subjects identified as having one or more of the ESR1 mutations before beginning treatment or that develop during treatment are administered an estrogen receptor antagonist (e.g., tamoxifen or fulvestrant). In some embodiments, subjects not found to have the ESR1 variants are not administered an estrogen receptor antagonist.

In some embodiments, patients currently undergoing cancer treatment (e.g., with an aromatase inhibitor such as, for example, exemestane, anastrozole and letrozole) are screened for the presence or absence of one or more mutations in ESR1. In some embodiments, subjects found to have the mutations are administered an estrogen receptor antagonist in addition to or instead of the aromatase inhibitor.

In some embodiments, assays for ESR1 mutations are repeated (e.g., before, during or after anticancer treatment). In some embodiments, assays are repeated daily, weekly, monthly, annually, or less often.

EXPERIMENTAL

The following examples are provided in order to demonstrate and further illustrate certain preferred embodiments and aspects of the present invention and are not to be construed as limiting the scope thereof.

Example 1 A. Methods

Clinical Study and specimen collection

Sequencing of clinical samples was performed under Institutional Review Board (IRB)-approved studies at the University of Michigan. Patients were enrolled and consented for integrative tumor sequencing, MI-ONCOSEQ (Michigan Oncology Sequencing Protocol, IRB #HUM00046018). Medically qualified patients 18 years or older with advanced or refractory cancer were eligible for the study. Informed consent details the risks of integrative sequencing and includes up-front genetic counseling. Informed consent was obtained from all subjects included in this study. Biopsies were arranged for safely accessible tumor sites. Needle biopsies were snap frozen in OCT and a longitudinal section was cut. Hematoxylin and eosin (H&E) stained frozen sections were reviewed by pathologists to identify cores with highest tumor content. Remaining portions of each needle biopsy core were retained for nucleic acid extraction.

Extraction of DNA and RNA

Genomic DNA from frozen needle biopsies and blood was isolated using the Qiagen DNeasy Blood & Tissue Kit, according to the manufacturer's instructions. Total RNA was extracted from frozen needle biopsies using the Qiazol reagent with disruption using a 5 mm bead on a Tissuelyser II (Qiagen), and purified using a miRNeasy kit (Qiagen) with DNase I digestion, according to the manufacturer's instructions. RNA integrity was verified on an Agilent 2100 Bioanalyzer using RNA Nano reagents (Agilent Technologies).

Preparation of next generation sequencing libraries

Transcriptome libraries were prepared using 1-2 μg of total RNA. Poly(A)+ RNA was isolated using Sera-Mag oligo(dT) beads (Thermo Scientific) and fragmented with the Ambion Fragmentation Reagents kit (Ambion, Austin, Tex.). cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to Illumina's TruSeq RNA protocol (Illumina). Libraries were size-selected for 250-300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) agarose gel, recovered using QIAEX II gel extraction reagents (Qiagen), and PCR-amplified using Phusion DNA polymerase (New England Biolabs). The amplified libraries were purified using AMPure XP beads (Beckman Coulter). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2000, (2×100 nucleotide read length). Reads that passed the chastity filter of Illumina BaseCall software were used for subsequent analysis.

Exome libraries of matched pairs of tumor/normal genomic DNAs were generated using the Illumina TruSeq DNA Sample Prep Kit, following the manufacturer's instructions. In brief, 1-3 μg of each genomic DNA was sheared using a Covaris S2 to a peak target size of 250 bp. Fragmented DNA was concentrated using AMPure XP beads, followed by end-repair, A-base addition, and ligation of the Illumina indexed adapters. The adapter-ligated libraries were electrophoresed on 3% Nusieve agarose gels (Lonza) and fragments between 300 to 350 bp were recovered using QIAEX II gel extraction reagents (Qiagen). Recovered DNA was amplified using Illumina index primers for 8 cycles, purified using AMPure XP beads, and the DNA concentration was determined using a Nanodrop spectrophotometer. 1 μg of the library was hybridized to the Agilent SureSelect Human All Exon V4 at 65° C. for 60 hr following the manufacturer's protocol (Agilent). The targeted exon fragments were captured on Dynal M-280 streptavidin beads (Invitrogen), and enriched by amplification with the Illumina index primers for 9 additional PCR cycles. PCR products were purified with AMPure XP beads and analyzed for quality and quantity using an Agilent 2100 Bioanalyzer and DNA 1000 reagents.

The publicly available software FastQC was used to assess sequencing quality. For each lane, the per-base quality scores were examined across the length of the reads. Lanes were deemed passing if the per-base quality score boxplot indicated that >85% of the reads had >Q20 for bases 1-100. In addition to the raw sequence quality, alignment quality was assessed using the Picard package. This allows monitoring of duplication rates and chimeric reads that may result from ligation artifacts; crucial statistics for interpreting the results of copy number and structural variant analysis.

Gene Fusion Detection

Paired-end transcriptome sequencing reads were aligned to the human reference genome (GRCh37/hgl9) using a RNA-Seq spliced read mapper Tophat2 (Kim, D. & Salzberg, S.L. Genome Biol 12, R72 (2011) (Tophat 2.0.4), with ‘--fusion-search’ option turned on to detect potential gene fusion transcripts. In the initial process, Tophat2 internally deploys an ultrafast short read alignment tool Bowtie (Version 0.12.8) to map the transcriptome data. Potential false positive fusion candidates were filtered out using ‘Tophat-Post-Fusion’ module. Further, the fusion candidates were manual examined for annotation and ligation artifacts. Junction reads supporting the fusion candidates were re-aligned using an alignment tool BLAT to reconfirm the fusion breakpoint. Full length sequence of the fusion gene was constructed based on supporting junction reads, and evaluated for potential open reading frames (ORF) using an ORF finder. Further, the gene fusions with robust ORFs, the amino acid sequences of the fused proteins were explored using the Simple Modular Architecture Research Tool (SMART) to examine the gain or loss of known functional domains in the fusion proteins.

Gene Expression

The BAM file ‘accepted hits.bam’ which was generated by the Tophat mapping module, was utilized to quantify the expression data, through Cufflinks (Trapnell, C. et al. Nat Protoc 7, 562-78 (2012)) (Version 2.0.2), an isoform assembly and RNA-Seq quantitation package. Structural features of 56,369 transcripts from the Ensemble resource (Ensemble66) was used as an annotation reference for quantifying expression of individual transcripts/isoforms. The ‘Max Bundle Length’ parameter was set to ‘10000000’ and ‘multi-read-correct’ is flagged on to perform an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.

Mutation Analysis

Whole-exome sequencing was performed on Illumina HiSeq 2000 or HiSeq 2500 in paired-end mode and the primary base call files were converted into FASTQ sequence files using the bcl2fastq converter tool bcl2fastq-1.8.4 in the CASAVA 1.8 pipeline. The FASTQ sequence files generated were then processed through an in-house pipeline constructed for whole-exome sequence analyses of paired cancer genomes. The sequencing reads were aligned to the reference genome build hg19, GRCh37 using Novoalign Multithreaded (Version2.08.02) (Novocraft) and converted into BAM files using SAMtools (Version 0.1.18) (Li, H. et al. Bioinformatics 25, 2078-9 (2009)). Sorting and indexing of BAM files utilized Novosort threaded (Version 1.00.01) and duplicates reads were removed using Picard (Version 1.74). Mutation analysis was performed using VarScan2 algorithms (Version2.3.2) (Koboldt, D. C. et al. Genome Res 22, 568-76 (2012)) utilizing the pileup files created by SAMtools mpileup for tumor and matched normal samples, simultaneously performing the pairwise comparisons of base call and normalized sequence depth at each position. For single nucleotide variant detection, filtering parameters including coverage; variant read support, variant frequency, P-value, base quality, homopolymer, and strandedness are applied. For indels analysis Pindel (Version 0.2.4) was used on tumor and matched normal samples and indels common in both samples were classified as germline and indels present in tumor but not in normal were classified as somatic. Finally, the list of candidate indels as well as somatic and/or germline mutations was generated by excluding synonymous SNVs. ANNOVAR (Wang, K., Li, M. & Hakonarson, H. Nucleic Acids Res 38, e164 (2010)) was used to functionally annotate the detected genetic variants and positions are based on Ensemble66 transcript sequences.

Tumor content for each tumor exome library was estimated from the sequence data by fitting a binomial mixture model with two components to the set of most likely SNV candidates on 2-copy genomic regions. The set of candidates used for estimation consisted of coding variants that (1) exhibited at least 3 variant fragments in the tumor sample, (2) exhibited zero variant fragments in the matched benign sample with at least 16 fragments of coverage, (3) were not present in dbSNP, (4) were within a targeted exon or within 100 base pairs of a targeted exon, (5) were not in homopolymer runs of four or more bases, and (6) exhibited no evidence of amplification or deletion. In order to filter out regions of possible amplification or deletion, we used exon coverage ratios to infer copy number changes, as described below. Resulting SNV candidates were not used for estimation of tumor content if the segmented log-ratio exceeded 0.2 in absolute value. Candidates on the Y chromosome were also eliminated because they were unlikely to exist in 2-copy genomic regions. Using this set of candidates, we fit a binomial mixture model with two components using the R package flexmix, version 2.3-8. One component consisted of SNV candidates with very low variant fractions, presumably resulting from recurrent sequencing errors and other artifacts. The other component, consisting of the likely set of true SNVs, was informative of tumor content in the tumor sample. Specifically, under the assumption that most or all of the observed SNV candidates in this component are heterozygous SNVs, we expect the estimated binomial proportion of this component to represent one-half of the proportion of tumor cells in the sample. Thus, the estimated binomial proportion as obtained from the mixture model was doubled to obtain an estimate of tumor content.

Copy number aberrations were quantified and reported for each gene as the segmented normalized log 2-transformed exon coverage ratios between each tumor sample and matched normal sample (Lonigro, R. J. et al. Neoplasia 13, 1019-25 (2011)). To account for observed associations between coverage ratios and variation in GC content across the genome, lowess normalization was used to correct per-exon coverage ratios prior to segmentation analysis. Specifically, mean GC percentage was computed for each targeted region, and a lowess curve was fit to the scatterplot of log 2-coverage ratios vs. mean GC content across the targeted exome using the lowess function in R (version 2.13.1) with smoothing parameter f=0.05.

Partially redundant sequencing of areas of the genome affords the ability for cross validation of findings. We cross-validated exome-based point mutation calls by manually examining the genomic and transcriptomic reads covering the mutation using the UCSC Genome Browser. Likewise, gene fusion calls from the transcriptome data can be further supported by structural variant detection in the genomic sequence data, as well as copy number information derived from the genome and exome sequencing.

Chemicals and Reagents

β-Estradiol, (Z)-4-Hydroxytamoxifen, (E/Z)-Endoxifen Hydrochloride Hydrate, and Fulvestrant were purchased from Sigma-Aldrich.

Plasmids and Cloning

cDNA for the wild type ESR1 was PCR amplified from a breast cell line MCF7 with the introduction of an N-terminal FLAG tag. cDNA encoding the relevant mutations of ESR1 were generated by site-directed mutagenesis (QuikChange, Agilent) and full-length constructs were fully sequenced. All the ESR1 variants were placed in the Lentivial vector pCDH (System Biosciences) for eukaryotic expression.

ERE-Luciferase Reporter Assay

For cell transfection experiments, HEK-293T cells were plated at a density of 1-2×10⁵ per well (24-well plates) in phenol red-free Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS) and antibiotics. Once cells attached, replaced medium with DMEM containing 10% charcoal-dextran treated FBS (HyClone) and cultured overnight. The next day, cells were transiently co-transfected with ESR1-expression plasmid at 50 ng/well and luciferase reporter constructs at 25 ng per well (SABiosciences) using the FuGene 6 reagent (Promega). The ER-responsive luciferase plasmid encoding the firefly luciferase reporter gene is driven by a minimal CMV promoter and tandem repeats of the estrogen transcriptional response element (ERE). A second plasmid constitutively expressing Renilla luciferase is served as an internal control for normalizing transfection efficiencies (Cignal ERE Reporter, SABiosciences). After transfection for 18 hrs, cells were serum-starved for a few hours before treatment with β-estradiol or anti-estrogen drugs. Cells were harvested 18 hr post-treatment, and luciferase activity was measured using the Dual-Luciferase Reporter Assay System (Promega). 1050 values were computed using the GraphPad Prizm application to fit a four parameter doseresponse curve.

Results

Advances in high-throughput sequencing technologies are beginning to establish a molecular taxonomy for a spectrum of human diseases and facilitate a move towards “precision medicine” (Chin, L., et al., Nat Med 17, 297-303 (2011); Meyerson, M., et al., Nat Rev Genet. 11, 685-96 (2010)). With regards to oncology, defining the mutational landscape of an individual patient's tumor leads to more precise treatment and management of cancer patients. Comprehensive clinical sequencing programs for cancer patients have been initiated at a variety of medical centers (Roychowdhury, S. et al. Sci Transl Med 3, 11 lral21 (2011); Welch, J. S. et al. JAMA 305, 1577-84 (2011)). In addition to the potential of identifying “actionable” therapeutic targets in cancer patients, these clinical sequencing efforts also shed light on acquired resistance mechanisms developed to targeted therapies (Gorre, M. E. et al. Science 293, 876-80 (2001); Korpal, M. et al. Cancer Discov (2013); Joseph, J. D. et al. Cancer Discov (2013)). ER is the primary therapeutic target in breast cancer and is expressed in 70% of cases (Ariazi, E. A., et al., Curr Top Med Chem 6, 181-202 (2006)). Drugs directly antagonizing ER such as tamoxifen and fulvestrant are a mainstay of breast cancer treatment, however approximately 30% of ER positive breast cancer exhibit de novo resistance while 40% acquire resistance to these therapies (Riggins, R. B., et al., Cancer Lett 256, 1-24 (2007)). In addition to anti-estrogen therapies, ER-positive breast cancer patients are also treated with aromatase inhibitors such as letrozole or exemestane (Lonning, P. E. & Eikesdal, H. P. Endocr Relat Cancer 20, R183-201 (2013)). Aromatase inhibitors block peripheral conversion of androgens to estrogen, and in post-menopausal women, lead to over a 98% decrease in circulating levels of estrogen. Like anti-estrogens, patients treated with aromatase inhibitors develop resistance, but presumably due to different mechanisms. Breast cancer patients that develop resistance to aromatase inhibitors, often still respond to anti-estrogen therapies (Ingle, J. N. et al. J Clin Oncol 24, 1052-6 (2006)). The molecular mechanisms of endocrine resistance in ER positive breast cancer continues to be an active area of research (Osborne, C. K. & Schiff, R. Mechanisms of endocrine resistance in breast cancer. Annu Rev Med 62, 233-47 (2011)).

The clinical sequencing program, called MI-ONCOSEQ (the Michigan Oncology Sequencing Program), enrolls patients with advanced cancer across all histologies (Welch et al., supra). Since April of 2011, it has enrolled over 200 patients by obtaining a current tumor biopsy with matched normal samples (blood and/or buccal swab). The samples are then subjected to integrative sequencing which includes whole exome sequencing of the tumor and matched normal, transcriptome sequencing, and as needed, low pass whole genome sequencing (Welch et al., supra). This combination of DNA and RNA sequencing technologies allows one to be relatively comprehensive with regards to the mutational landscape of coding genes including point mutations, indels, amplifications, deletions, gene fusions/translocations, and outlier gene expression. These results are generated within a 5 to 7 week time frame and are presented at an institutional “precision medicine tumor board” to deliberate upon potentially actionable findings.

As part of the MI-ONCOSEQ program, 11 patients with metastatic ER-positive breast cancer were subjected to sequencing analysis (Tables 1 and 2). A diverse array of aberrations were identified in individual patients, including mutations in PIK3CA (n=4), BRCA1 aberrations (n=2), FGFR2 aberrations (n=2) (Wu, Y. M. et al. Identification of Targetable FGFR Gene Fusions in Diverse Cancers. Cancer Discov 3, 636-647 (2013)), NOTCH2 frameshift deletion (n=1), cyclins and associated cyclin-dependent kinase aberrations (n=3), and MDM2 amplification/overexpression (n=1). Aberrations were also found frequently in the tumor suppressor TP53 (n=6), DNA mismatch repair gene MSH2 (n=1), and epigenetic regulators (n=2) including ARID2, ARID1A, SMARCA4, among others. The complete spectrum of somatic mutations with associated expression levels and copy number alterations in the index cases are given in Tables 3 and 4, and FIG. 5. Two of the index cases, MO_(—)1031 and MO_(—)1051, exhibited a high level of mutations consistent with the “Signature B” identified in a whole genome study of mutational processes in breast cancer (Nik-Zainal, S. et al. Cell 149, 979-93 (2012)). There were 39 gene fusions identified in the 6 index cases with 11 encoding in-frame fusion proteins (Table 5 and FIG. 6), including an activating fusion of FGFR2-AFF3 (Wu et al., supra).

Nonsynonymous mutations were identified in the LBD of ESR1 (n=6). The six index patients MO_(—)1031, MO_(—)1051, MO_(—)1069, MO_(—)1129, MO_(—)1167, and MO_(—)1185 had LBD mutations in amino acids p.Leu536Gln, p.Tyr537Ser, p.Asp538Gly, p.Tyr537Ser, p.Asp538Gly, and p.Tyr537Ser, respectively. The respective mutation in each case was detected by whole exome sequencing of the tumor relative to matched normal, as well as corroborated with whole transcriptome sequencing since ESR1 was expressed at moderate to high levels (Table 3). The clinical histories of the index patients are depicted as timelines in FIG. 1. For three of the patients (MO_(—)1051, MO_(—)1069, and MO_(—)1129), primary diagnostic material showed that the ESR1 mutations were not present at an earlier stage, indicating that they were acquired after endocrine therapy (FIG. 1 and Table 3). All of the index patients were treated with anti-estrogens (tamoxifen and/or fulvestrant) and aromatase inhibitors (letrozole, anastrozole, and/or exemestane). Two of the patients also had an oophorectomy. Comparison of the mutations present in each primary versus post-treatment pair showed a significant number of shared mutations in both samples of the pair, including activating mutations in PIK3CA in two of the cases. Thus, it is clear that the index patients presented with recurrent disease of the original primary tumor surviving in an estrogen deprived state, and presenting with acquired ESR1 mutations. Of note, neither ESR1 amplifications nor gene fusions were observed in these patients.

The 5 novel LBD mutations of ESR1 identified in this study are depicted in FIG. 2. Each occur in the vicinity of the synthetic mutations of ESR1 which are inverted in response to tamoxifen and involve amino acid alterations p.Met543Ala and p.Leu544Ala (Inv-mut-AA2) (Feil, R., et al., Biochem Biophys Res Commun 237, 752-7 (1997)) and served as a positive control for our subsequent in vitro studies. It was next assessed whether tumor types other than ER positive metastatic hormone-resistant breast cancer also acquire ligand binding mutations in ESR1. The Cancer Genome Atlas Project (TCGA), which has generated whole exome data on 27 tumor types across at least 4000 individual samples was utilized. LBD mutations of ESR1 were not detected in the 390 ER-positive breast cancers sequenced by TCGA, as these were primary resection samples before hormonal treatment (TCGA. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012)), nor have we detected ESR1 mutations in a cohort of 80 triple negative breast carcinoma transcriptomes (unpublished data). As the LBD mutations of ESR1 we identified were somatic and acquired after treatment, we next assessed whether they were dependent on estrogen for activation. We cloned into expression vectors each of the five ESR1 mutations identified in this study (p.Leu536Gln, p.Tyr537Ser, p.Asp538Gly, p.Tyr537Cys, and p.Tyr573Asn) and subsequently co-transfected them into HEK-293 cells with an ERE-luciferase reporter system. Steroid hormone deprived cells were then exposed to β-estradiol for 24 hours and ER reporter levels assessed. Unlike wild-type ER which had little ER reporter activity in the absence of ligand, all 5 of the ESR1 mutations exhibited strong constitutive activation of the ER reporter that was not markedly enhanced with β-estradiol (FIG. 3). This indicated that each of the mutations developed in the context of evolution during an estrogen deprived state. Consistent with this, a whole genome sequencing study of 46 cases of estrogen receptor positive breast cancer patients on two aromatase inhibitor trials did not identify any of these ESR1 mutations in the pretreatment samples analyzed (Ellis, M. J. et al. Nature 486, 353-60 (2012)).

Next, it was assessed whether anti-estrogen therapies affected the functional activity of these LBD mutations. As inhibition effects can be influenced by level of ectopic estrogen receptor expression, a dose response study of expression plasmid was performed 50 ng was selected for the following experiments (Huang, H. J., et al., Mol Endocrinol 16, 1778-92 (2002)) (FIG. 7). Wild-type ER was inhibited in a dose-dependent fashion by the anti-estrogens 4-hydroxytamoxifen, fulvestrant and endoxifen (FIGS. 4, 8, 9, and 10). In addition, the synthetic ESR1 mutation (Inv-mut-AA2) was activated in a dose-dependent fashion by these anti-estrogens (FIG. 4), which has been reported previously (Feil, et al., Biochem Biophys Res Commun 237, 752-7 (1997)). Each of the 5 LBD mutations of ESR1 identified in this study was inhibited by tamoxifen and fulvestrant in a dose-dependent fashion and do not exhibit the inverted response to antiestrogens that the synthetic mutation Inv-mut-AA2 does. It is possible that these mutations did not arise under selective pressure of anti-estrogen treatment, but rather in the context of an estrogen deprivation setting such as treatment with aromatase inhibitors and/or oophorectomy. The IC50s for both 4-hydroxytamoxifen and fulvestrant were 2 to 4 fold higher for all the mutants compared to wild type ESR1. Fulvestrant exhibited greater maximal inhibition than 4-hydroxytamoxifen for all the mutants tested (FIGS. 8 and 9).

The ESR1 mutations identified in this study cluster near the beginning of helix 12 (FIG. 2). Structural studies have demonstrated a key role in the position of helix 12 in the response of the estrogen receptor to agonists and antagonists (Shiau, A. K. et al. Cell 95, 927-37 (1998), and p.Tyr537 has been postulated to form a capping motif contributing to activity of the receptor (Skafar, Cell Biochem Biophys 33, 53-62 (2000)). Specifically the p.Tyr537Ser mutant has been reported to have higher affinity for estrogen than wild type and interacts with the SRC 1 coactivator in the absence of ligand (Carlson et al., Biochemistry 36, 14897-905 (1997); Weis et al., Mol Endocrinol 10, 1388-98 (1996)). Several studies using experimental mutagenesis have implicated the same three residues identified here as critical determinants of transcriptional activity of the receptor (Carlson et al., supra; Pearce, et al., J Biol Chem 278, 7630-8 (2003); Zhao, C. et al. J Biol Chem 278, 27278-86 (2003)).

As estrogen therapy has been shown to have positive effect in treating aromatase inhibitor resistant advance breast cancers, we tested the effect of low to high dose estrogen on the activity of the mutants in the transient luciferase reporter assay (FIG. 11) (Ellis, M. J. et al. JAMA 302, 774-80 (2009); Swaby, R. F. & Jordan, Clin Breast Cancer 8, 124-33 (2008)). The results do not suggest the effectiveness of this therapy is via directly influencing the transcriptional activity of these mutants, if present in the responding patients.

The experiments described herein revealed either de novo driver mutations and/or potential acquired mutations in breast cancer such as PI3K activation, PAK1 amplification, and FGFR fusion/amplification which have been described earlier (Wu, Y. M. et al. Cancer Discov 3, 636-647 (2013); Kan, Z. et al. Nature 466, 869-73 (2010); Shrestha, Y. et al. Oncogene 31, 3397-408 (2012). Focal amplification of MDM2 (a negative regulator of p53 which is targetable) and copy gains of gonadotropin-releasing hormone receptor (GNRHR) were identified.

Since the LBD mutations of ESR1 identified in this study are constitutively active, they can function in the absence of ligand, and maintain ER signaling. In 1997, an LBD mutation of ESR I, p.Tyr537Asn, was detected in a single patient with Stage 1V metastatic breast cancer who had been treated with diethylstibesterol—but since then, this mutation has been considered very rare (Barone et al., Clin Cancer Res 16, 2702-8 (2010)). With the advent of widespread aromatase inhibitor therapy, mutation of the ESR1 LBD is likely a common mechanism of resistance that develops in low estrogen states. LBD mutations of ESR1 were detected somatically in four out of 373 cases of endometrial cancers (Kandoth, C. et al. Nature 497, 67-73 (2013)).

This example demonstates that LBD mutations do not develop in the context of anti-estrogen treatment, since the mutated ESR1 variants continue to be responsive to direct ER antagonists such as tamoxifen and fulvestrant. This is consistent with clinical reports showing that patients that develop resistance to aromatase inhibitors still respond to antiestrogen treatment (Ingle, J. N. et al. Fulvestrant in women with advanced breast cancer after progression on prior aromatase inhibitor therapy: North Central Cancer Treatment Group Trial N0032. J Clin Oncol 24, 1052-6 (2006)).

Accession Codes.

Sequence data have been deposited at the dbGAP, which is hosted by the National Center for Biotechnology Information (NCBI), under accession dbGAP phs000602.v1.p1, and CSER Clinical Sequencing Exploratory Research Program for the NIH-NHGRI grant (1UM1HG006508).

TABLE 1 Clinical sequencing of eleven metastatic ER-positive breast cancer cases. ER/PR/ #SNV/ Case Age ERBB2 Treatments^(a) #Fusion Genetic aberrations^(b) MO_1031 41 +/+/− Tamoxifen, 266/18 ESR1 (p.Leu536Gln), gene copy Letrozole, gains of FGFR1, FGFR2, Fulvestrant CCND1, and GNRHR MO_1051 31 +/−/− Oophorectomy, 248/5  ESR1 (p.Tyr537Ser), PIK3CA Letrozole, (p.His1047Arg), TP53 Fulvestrant (p.Gly199Glu), FGFR2-AFF3 fusion MO_1069 62 +/+/− Tamoxifen, 74/9 ESR1 (D538G), ARID2 Letrozole, (p.Glu245*), gene copy losses of Fulvestrant TP53, BRCA1, RB1, ARID1A, and SMARCA4 MO_1129 44 +/+/− Tamoxifen, 32/3 ESR1 (p.Tyr537Ser), PIK3CA oophorectomy, (p.Glu542Lys), gene copy gains Anastrozole, of CCND1 and PAK1 Fulvestrant, Exemestane MO_1030 78 +/+/− Tamoxifen (short), 26/2 PIK3CA (p.Glu545Ala), TP53 Anastrozole, copy loss Fulvestrant MO_1068 65 +/−/− Tamoxifen,  83/10 PIK3CA (p.His1047Arg), TP53 Anastrozole (p.Glu51*), MSH2 copy loss MO_1090 52 +/+/− Tamoxifen,  28/11 No significant drivers identified Anastrozole MO_1107 46 +/+/− Tamoxifen,  63/12 BRCA1 (c.5385_5386insC), oophorectomy, frameshift deletions in TP53, Anastrozole, SMARCA4, and NF1 Fulvestrant, Exemestane MO_1167 60 +/−/− Tamoxifen, 47/3 ESR1 (p.Asp538Gly) Letrozole MO_1185 58 +/+/− Tamoxifen, 88/1 ESR1 (p.Tyr537Ser), CDH1 Letrozole, (p.Gln641*), NOTCH2 Fulvestrant, (frameshift deletion), TP53 copy Exemestane loss TP_2004^(c) 52 +/−/− Tamoxifen (short)  29/22 MDM2 gene amplification, gene copy losses of CDKN2A and CDKN2B Notes: ^(a)Only anti-estrogen related treatments are listed in table. Patients also received chemotherapies, radiation, or mastectomy in the interim between diagnosis and MI-ONCOSEQ sequencing. ^(b)Amino acid substitutions caused by nonsynonymous somatic mutations are marked in parentheses. ^(c)TP_2004 is a male patient.

TABLE 2 Read % PF PhiX % % > Gb Case ID Lib ID Library Type Sample Length Clusters Error Q30 # Reads % Aligned Aligned MO_1185 SI_6764 Transcriptome Tumor Biopsy-2013 2 × 111 90.6 0.24 84.7 83957912 90.6 8.44 MO_1185 SI_6828 Exome Capture Tumor Biopsy-2013 2 × 111 92.0 0.22 91.0 192597898 91.7 19.60 MO_1185 SI_6830 Exome Capture Normal Blood-2013 2 × 111 92.0 0.22 91.0 137187312 92.5 14.09 MO_1167 SI_6652 Transcriptome Tumor Biopsy-2013 2 × 111 91.2 0.25 89.7 118377118 92.3 11.98 MO_1167 SI_6609 Exome Capture Tumor Biopsy-2013 2 × 111 95.0 0.19 95.2 229166770 91.9 24.17 MO_1167 SI_6610 Exome Capture Tumor Biopsy-2013 2 × 111 95.0 0.19 95.2 150585064 93.3 15.88 MO_1129 SI_6664 Transcriptome Tumor Biopsy-2013 2 × 126 93.2 0.56 90.7 110783125 93.3 13.03 MO_1129 SI_6191 Exome Capture Tumor Biopsy-2013 2 × 101 91.7 0.72 89.6 216483626 91.1 19.92 MO_1129 SI_6192 Exome Capture Normal Blood-2013 2 × 101 91.7 0.72 89.6 135084370 91.6 12.50 MO_1129 SI_6580 Exome Capture Tumor FFPE-2001 2 × 111 92.4 0.58 90.2 113985464 94.4 11.95 MO_1089 SI_5257 Transcriptome Tumor Biopsy-2012 2 × 101 92.5 0.63 86.3 108932482 91.2 10.03 MO_1089 SI_5259 Exome Capture Tumor Biopsy-2012 2 × 101 93.5 0.54 88.7 228128358 92.1 21.22 MO_1089 SI_5260 Exome Capture Normal Blood-2012 2 × 101 93.5 0.54 88.7 143597568 93.0 13.49 MO_1089 SI_6666 Exome Capture Tumor FFPE-1994 2 × 126 93.2 0.56 90.7 115997626 96.2 11.28 MO_1051 SI_5091 Transcriptome Tumor Biopsy-2012 2 × 101 89.2 0.67 87.4 102882633 91.2 9.47 MO_1051 SI_5121 Exome Capture Tumor Biopsy-2012 2 × 101 92.3 0.86 87.4 209297646 92.1 19.47 MO_1051 SI_5080 Exome Capture Normal Blood-2012 2 × 101 90.0 0.69 88.4 193338100 89.0 17.38 MO_1051 SI_5447 Exome Capture Tumor FFPE-2005 2 × 101 93.3 1.04 83.3 176710228 89.2 15.91 MO_1031 SI_5256 Transcriptome Tumor Biopsy-2012 2 × 101 91.8 0.61 84.7 101227958 92.4 9.45 MO_1031 SI_5261 Exome Capture Tumor Biopsy-2012 2 × 101 93.7 0.67 86.8 150236180 91.4 13.87 MO_1031 SI_5262 Exome Capture Normal Blood-2012 2 × 101 93.7 0.67 86.8 221415120 91.6 20.48

TABLE 3 Amino Acid Present in Expression COSMIC AVISIFT Case ID Gene Change Chr Coord Ref Var FFPE (FPKM) @ Pos Score MO 1031 HLA-A p.A182V 6 29911246 C T NA 323.8 0 0.08 MO 1031 ESR1 p.L536Q 6 152419920-1 TC AG NA 55.5 0 0 MO 1031 GPS2 p.Q226X 17 7216747 G A NA 52.7 0 0 MO 1031 PATZ1 p.R214W 22 31740949 G A NA 42.1 0 0 MO 1031 MTOR p.F319L 1 11308035 G C NA 15.6 0 0.65 MO 1031 RNF43 p.E712Q 17 56434880 C G NA 14.8 0 0 MO 1031 CRKL p.S112C 22 21288090 C G NA 11.4 0 0.02 MO 1031 BIRC2 p.K102N 11 102220891 G C NA 11.4 0 0.02 MO 1031 AKAP9 p.S403F 7 91630403 C T NA 10.3 0 0 MO 1031 AKAP9 p.P1393S 7 91662316 C T NA 10.3 0 0.51 MO 1031 PSIP1 p.Q384X 9 15469011 G A NA 10.1 0 0 MO 1031 G 

 R124 p.A394V 8 37690611 C T NA 8.7 0 0.36 MO 1031 KDM5A p.R1121T 12 418985 C G NA 7.2 0 0.01 MO 1031 NCOA1 p.S1320C 2 249 

 0919 C G NA 4.9 0 0 MO 1031 ARID2 p.E1315K 12 46245849 G A NA 3.1 0 0.01 MO 1031 BRIP1 p.M1970I 17 59763192 C T NA 2.0 0 0 MO 1031 ASXL2 p.E1178Q 2 25965674 C G NA 1.7 0 0.02 MO 1031 APC p.D1558N 5 112175953 G A NA 1.1 0 0.09 MO 1031 FAM123B p.Q1098X X 63409875 G A NA 0. 

  0 0.31 MO 1031 BLK p.M164I 8 11414186 G A NA 0.1 0 0.11 MO 1031 IRS4 p.S49F X 107979429 G A NA 0.0 0 0 MO 1031 FN1 p.R1162T 2 216262435 C G NA 901.7 0 0.01 MO 1031 KIAA0 

 13 p.R944L 10 75554320 G T NA 400.5 0 0.06 MO 1031 DLG5 p.R1685C 10 79565534 G A NA 376.4 1 0 MO 1031 FLNA p.R1951W X 153581931 G A NA 276.3 0 0 MO 1031 ERI3 p.V7L 1 44788522 C G NA 231.6 0 0 MO 1031 NUDT5 p.S199C 10 12209765 G C NA 215.4 0 0.05 MO 1031 CLTC p.E33Q 17 57721691 G C NA 182.2 0 0.03 MO 1031 ANXA7 p.S301X 10 75143015 G C NA 166.1 0 0.38 MO 1031 C14orf166 p.R65K 14 52460448 G A NA 156.3 0 1 MO 1031 MRPL38 p.S263C 17 73895678 G C NA 148.7 0 0.02 MO 1031 IGLV2-23 p.A27V 22 23040632 C T NA 141.3 0 0.01 MO 1031 SCRIB p.E686K 8 144890838 C T NA 107.1 0 0.23 MO 1031 S100A13 p.L71F 1 153591457 G A NA 101.3 0 0 MO 1031 CTSZ p.D72H 20 57581470 C G NA 82.9 0 0.01 MO 1031 RAB11FIP1 p.E931K 8 37729529 C T NA 80.2 0 0 MO 1031 DLGAP4 p.S225C 20 35060794 C G NA 71.7 0 0.01 MO 1031 FAAH p.R260C 1 46871459 C T NA 60.6 0 0 MO 1031 RBM 

  p.M10 

 7I 3 50114455 G A NA 60.4 0 0.06 MO 1031 DHTKD1 p.V298M 10 12131159 G A NA 57.1 0 0.63 MO 1031 PARP12 p.R242T 7 139756691 C G NA 56.9 0 0.27 MO 1031 MAN2A2 p.I71M 15  

 1448561 C G NA 55.4 0 0 MO 1031 MAEA p.E27D 4 1305778 G C NA 53.2 0 0 MO 1031 USP34 p.E2101Q 2 61475739 C G NA 52.4 0 0 MO 1031 TTC17 p.E329Q 11 43419590 G C NA 51.8 0 0.05 MO 1031 MUC19 p.H954D 12 40836890 C G NA 49.1 0 0.63 MO 1031 PSMC2 p.E18 

 K 7 10300384 

  G A NA 48.1 0 0.57 MO 1031 POR p.R554Q 7 75615159 G A NA 44.8 0 0.09 MO 1031 CNKSR1 p.A534G 1 26515099 C G NA 44.6 0 0.25 MO 1031 MAPKAP1 p.R467T 9 128201227 C G NA 43.4 0 0 MO 1031 ADAM9 p.S38L 8 38865420 C T NA 41.8 0 0.13 MO 1031 CTNN 

 L1 p.D274N 20 36405816 G A NA 41.7 0 0.34 MO 1031 VPS1 

  p.E614Q 20 2845214 G C NA 39.9 0 0.22 MO 1031 VPS1 

  p.E684K 20 2845839 G A NA 39.9 0 0.01 MO 1031 RTKN p.G314S 2 74655775 C T NA 39.7 0 0 MO 1031 SFSWAP p.E523Q 12 132241036 G C NA 38.8 0 0.16 MO 1031 LONP1 p.I700M 19 5694826 G C NA 38.6 0 0.0 

  MO 1031 FNBP4 p.K938N 11 47741630 C G NA 38.2 0 0.02 MO 1031 UPF3A p.S50F 13 115047263 C T NA 33.4 0 0.06 MO 1031 PTPN12 p.I316T 7 77247804 T C NA 33.3 0 0.39 MO 1031 CUX1 p.E1492K 7 101892278 G A NA 27.3 0 0 MO 1031 NOL11 p.C144S 17 65717611 G A NA 27.1 0 0.07 MO 1031 CYP27A1 p.S280F 2 219677467 C T NA 27.1 0 0.02 MO 1031 ATP6V1 

 1 p.Q244H 2 71188770 G C NA 25.5 0 0 MO 1031 GMPR2 p.E204K 14 24706513 G A NA 24.4 0 0 MO 1031 SPTAN1 p.Q1980K 9 131386727 C A NA 24.0 0 0 MO 1031 SPTAN1 p.S2138C 9 131388818 C G NA 24.0 0 0 MO 1031 IVNS1ABP p.D77N 1 185278187 C T NA 23.9 0 0.32 MO 1031 LRP1 p.E270K 12 57539240 G A NA 23.6 0 0.13 MO 1031 TMEM129 p.S105Y 4 1720246 G T NA 23.4 0 0.03 MO 1031 FARP1 p.D153N 13 99030133 G A NA 22.2 0 0.02 MO 1031 KRT10 p.E169K 17 38978333 C T NA 22.2 0 0.25 MO 1031 SLC27A4 p.D127N 9 131108651 G A NA 21.1 0 0.08 MO 1031 HDAC11 p.P13S 3 13522251 C T NA 20.2 0 0 MO 1031 FAM193A p.K878E 4 2698318 A G NA 19.8 0 0 MO 1031 FAM100B p.S83C 17 74266339 C G NA 19.3 0 0 MO 1031 STAU2 p.M429I 8 74439971 C G NA 18.9 0 MO 1031 FAM84B p.Q129R 8 127569249 T C NA 18.6 0 0.34 MO 1031 SIN3A p.S689C 15 75688626 G C NA 18.4 0 0.03 MO 1031 NRP1 p.I121M 10 33559670 G C NA 17.6 0 0 MO 1031 PDCD7 p.L3V 15 65426113 G C NA 16.4 0 0 MO 1031 FRMD8 p.E462K 11 65178820 G A NA 16.2 0 0 MO 1031 SDCCAG8 p.G44A 1 243433470 G C NA 16.1 0 0.36 MO 1031 MBD5 p.Q987X 2 149241119 C T NA 15.6 0 0 MO 1031 RALGAPB p.D79H 20 37121621 G C NA 15.6 0 0 MO 1031 CAND1 p.E870X 12 67700058 G T NA 15.1 0 0 MO 1031 CEP250 p.L682V 20 34065878 C G NA 14.9 0 0 MO 1031 HSD17B8 p.E243K 6 33174184 G A NA 14.6 0 0.01 MO 1031 BAZ1A p.E1246Q 14 35233953 C G NA 14.6 0 0.3 MO 1031 PUM1 p.E249K 1 31468043 C T NA 14.6 0 0.09 MO 1031 RILPL1 p.M134I 12 124008100 C A NA 14.0 0 0.31 MO 1031 LACTB2 p.E65K 8 71574062 C T NA 13.8 0 0.16 MO 1031 LRIG1 p.T717M 3 66433747 G A NA 13.0 0 0.02 MO 1031 RNF6 p.E266K 13 26789223 C T NA 12.8 0 0.03 MO 1031 DDX58 p.R6Q  

  32526148 C T NA 12.7 0 0.02 MO 1031 UNKL p.E312D 16 1444133 C G NA 12.6 0 0.08 MO 1031 UNKL p.S246X 16 1448940 C T NA 12.6 0 0 MO 1031 LRBA p.L2000V 4 151520207 G C NA 12.4 0 0.14 MO 1031 LRBA p.F1979L 4 151520268 G C NA 12.4 0 0.01 MO 1031 HEATR5A p.L429F 14 31855668 G A NA 12.4 0 0 MO 1031 PRR12 p.L1355V 19 50102913 C G NA 12.1 0 0.14 MO 1031 UGGT1 p.I782M 2 128914911 C G NA 12.0 0 0.02 MO 1031 SLC10A3 p. 

 441E X 153715959 G C NA 12.0 0 0.42 MO 1031 PDLIM2 p.R243W 8 22447218 C T NA 11.8 0 0 MO 1031 PVRL4 p.D338H 1 161044152 C G NA 11.4 0 0.05 MO 1031 ZNHIT2 p.E111Q 11 64884795 C G NA 11.3 0 0.22 MO 1031 CMAHP p.L152F 6 25109797 G A NA 11.0 0 0.02 MO 1031 CNIH2 p.E114K 11 66050747 G A NA 10.5 0 0.02 MO 1031 CTAGE5 p.S661C 14 39 

 16944 C G NA 10.5 0 0 MO 1031 MMP19 p.S430L 12 56231058 G A NA 10.3 0 0.01 MO 1031 MREG p.R165K 2 216810310 C T NA 9.8 0 0 MO 1031 SLCO2A1 splice acc. 3 133692670 C G NA 9.6 0 MO 1031 C7orf13 p.A36P 7 156433243 C G NA 9.5 0 MO 1031 NUP160 p.D449Y 11 47840943 C A NA 8.6 0 0.02 MO 1031 PNPLA7 p.S555C 9 140395161 G C NA 8.5 0 0 MO 1031 GCDH p.P51R 19 13003198 C G NA 8.5 0 0.32 MO 1031 RNF115 p.E238K 1 145687020 G A NA 8.3 0 0.1 MO 1031 MFSD11 p.R304C 17 74771114 C T NA 8.1 0 0 MO 1031 BZRAP1 p.K1347N 17 56386592 C A NA 8.0 0 0 MO 1031 SNX27 p.D283H 1 151634687 G C NA 7.8 0 0 MO 1031 ZB 

 B42 p.M1I 14 105267537 G A NA 7.8 0 0 MO 1031 ZB 

 B42 p.E2K 14 105267538 G A NA 7.8 0 0.01 MO 1031 ZB 

 B42 p.E96K 14 105267820 G A NA 7.8 0 0 MO 1031 TTF1 p.K17N 9 135278158 C A NA 7.5 0 0 MO 1031 TMEM106B p.T234R 7 12271477 C G NA 7.4 0 0.24 MO 1031 SMARCC1 p.D284N 3 47752241 C T NA 7.3 0 0 MO 1031 INTS6 p.I3M 13 52026653 G C NA 7.3 0 0 MO 1031 AC008073.6.1 p.Q107X 2 24360929 C T NA 7.0 0 0.24 MO 1031 ZNF791 p.R544T 19 12739974 G C NA 6.8 0 0 MO 1031 SMG1 p.Q1779E 16 18861397 G C NA 6.7 0 0.96 MO 1031 INTS2 p.E759K 17 5 

 58371 C T NA 6.5 0 0.26 MO 1031 LRRC1 p.L314F 6 53769212 G C NA 6.5 0 0 MO 1031 CEP76 p.C612Y 18 12674541 C T NA 6.1 0 MO 1031 ZCCHC2 p.R214Q 18 60191298 G A NA 6.1 0 0 MO 1031 SP 

 CE1 p.L521V 3 113176079 G C NA 6.0 0 0.18 MO 1031 LY86 p.I78M 6 6626536 C G NA 6.0 0 0.23 MO 1031 CACNB1 p.G169C 17 37343092 G A NA 6.0 0 0 MO 1031 ARHGAP29 p.E185K 1 94671197 C T NA 6.0 0 0.06 MO 1031 RND1 p.S230Y 12 49251789 G T NA 5.7 0 0 MO 1031 ZCCHC3 p.E221K 20 178888 G A NA 5.6 0 0.03 MO 1031 SMOX p.S84C 20 4158040 C G NA 5.5 0 0 MO 1031 LENG9 p.E1 

 Q 19 54974190 C G NA 5.4 0 0.23 MO 1031 ZBTB1 p.M653I 14 64990181 G A NA 5.0 0 0.03 MO 1031 OBSCN p.Q1409X 1 228492156 C T NA 4.9 0 0.19 MO 1031 ZNF564 p.L237F 19 12638213 G A NA 4.8 0 0.7 MO 1031 PAFAH2 p.F278L 1 26301066 G C NA 4.8 0 0.47 MO 1031 GBP4 p.M542I 1 89652097 C T NA 4.6 0 0.94 MO 1031 ELMO1 p.G559E 7 36927203 C T NA 4.6 0 0 MO 1031 RPGR p.E512K X 38150250 C T NA 4.5 0 0.01 MO 1031 RAPH1 p.P1077T 2 204304684 G T NA 4.5 0 0 MO 1031 RGL4 p.R441Q 22 24040460 G A NA 4.5 0 0.58 MO 1031 RNF32 p.K94N 7 156447277 G C NA 4.5 0 0 MO 1031 KMO p.S171L 1 241725529 C T NA 4.3 0 0 MO 1031 TMOD3 p.S127Y 15 52179882 C A NA 4.2 0 0 MO 1031 MEX3A p.G459S 1 156046553 C T NA 4.0 0 MO 1031 KIF21A p.S1258L 12 39711971 G A NA 4.0 0 0 MO 1031 FAM179B p.H1193D 14 45497451 C G NA 3.8 0 1 MO 1031 DOCK10 p.D744H 2 225714229 C G NA 3.7 0 0 MO 1031 FMNL2 p.K217T 2 153431703 A C NA 3.7 0 0.03 MO 1031 FUT2 p.S52X 19 49206368 C G NA 3.4 0 0.01 MO 1031 ZCCHC14 p.L526P 16 87446339 A G NA 3.3 0 0 MO 1031 ZSWIM4 p.E232D 19 13915946 G C NA 3.3 0 0.02 MO 1031 PCLR2M p.T126P 15 58001174 A C NA 3.2 0 0.01 MO 1031 DET1 p.S169L 15 89074464 G A NA 3.2 1 0 MO 1031 SLC35D1 p.F145S 1 67516146 A G NA 3.1 0 0.01 MO 1031 CHIC1 p.X218S X 72900839 G C NA 2.9 0 0.86 MO 1031 SEMA3E p.E764Q 7 82996940 C G NA 2.9 0 0.02 MO 1031 ATG2B p.K11N 14 96829281 C G NA 2.9 1 0.04 MO 1031 FAT3 p.E2994X 11 92538402 G T NA 2.8 0 0.17 MO 1031 POPDC2 p.I154M 3 19378809 G C NA 2.3 0 0 MO 1031 SLIT3 p.T958S 5 168127656 G C NA 2.3 0 0.23 MO 1031 SYNPO2 p.R1088H 4 119978566 G A NA 2.2 0 0.26 MO 1031 VCPIP1 p.S545C 8 67577560 G C NA 2.2 0 0.02 MO 1031 FAM184B p.E73K 4 17711192 C T NA 2.1 0 0.01 MO 1031 RASA2 p.S323L 3 141289858 C T NA 2.1 0 0.2 MO 1031 C3orf67 p.S326L 3 58849525 G A NA 2.0 0 0.14 MO 1031 C1orf167 p.Q1046E 1 11844289 C G NA 2.0 0 0 MO 1031 ANKS1B p.G573E 12 99793447 C T NA 2.0 0 0.17 MO 1031 ZNF837 p.S376L 19 58879573 G A NA 1.9 0 0 MO 1031 NCOA7 p.E628K 6 126211082 G A NA 1.8 0 0 MO 1031 STXBP5 p.S973L 6 147685247 C T NA 1.8 0 0 MO 1031 BCO2 p.N134Y 11 112064303 A T NA 1.8 0 0.02 MO 1031 CRLF3 p.I389L 17 29111369 G A NA 1.6 0 MO 1031 TM 

 SF2 p.F148L 19 19380536 G T NA 1.6 0 0.89 MO 1031 ALPK3 p.E1722Q 15 85407731 G C NA 1.5 0 0 MO 1031 ZNF717 p.A312S 3 75787840 C A NA 1.2 0 0.32 MO 1031 ZNF717 p.V286I 3 75787918 C T NA 1.1 0 0.21 MO 1031 ZNF717 p.Y283C 3 75787926 T C NA 1.1 0 0.01 MO 1031 TTLL7 p.S287L 1 84385422 G A NA 1.1 0 0.07 MO 1031 TET3 p.E913K 2 74320668 G A NA 1.1 0 0.11 MO 1031 ACACB p.I1273F 12 109661644 A T NA 1.1 0 0 MO 1031 ADAMTSL3 p.G1502E 15 84694037 G A NA 1.0 0 0 MO 1031 FAM161A p.E114Q 2 62069339 C G NA 0.8 0 0 MO 1031 RGS9 p.D65E 17 63154453 C G NA 0.8 0 0.03 MO 1031 SCML1 p.S188F X 17768273 C T NA 0.8 0 0.01 MO 1031 CSF2RB p.P343S 22 37328821 C T NA 0.7 0 0 MO 1031 CYP7B1 p.S293F 8 65527762 G A NA 0.6 0 0 MO 1031 BTBD11 p.Q163H 12 107713206 G C NA 0.5 0 0.19 MO 1031 CCT6B splice donor 17 33269814 C T NA 0.5 0 MO 1031 PRDM5 p.E108K 4 12176040 

  C T NA 0.5 10 0 MO 1031 MYO15A p.E3242Q 17 18067089 G C NA 0.4 0 0.05 MO 1031 TAOK1 p.S826Y 17 27869955 C A NA 0.4 0 0 MO 1031 COL28A1 p.I779M 7 7415114 G C NA 0.4 0 0 MO 1031 FREM2 p.O2473K 13 39433625 C A NA 0.4 0 0.3 MO 1031 GABRA3 p.N406I X 151336962 T A NA 0.4 0 0.01 MO 1031 RUFY4 p.R422K 2 218940420 G A NA 0.3 0 0.42 MO 1031 RP11-8F2.7.1 p.E87Q 3 156570767 G C NA 0.3 0 0.25 MO 1031 ICAM5 p.S70L 19 10401874 C T NA 0.3 0 0.67 MO 1031 LCTL p.S111Y 15 66856287 G T NA 0.3 0 0 MO 1031 TMEM151A p.E257K 11 66062486 G A NA 0.3 0 0 MO 1031 RYR1 p.S1172L 19 38959739 C T NA 0.2 0 0.41 MO 1031 MACC1 p.Q488E 7 20193522 G C NA 0.2 0 0 MO 1031 ARPP21 p.S804R 3 35835423 C G NA 0.2 0 0.04 MO 1031 CCIN p.M409I 9 36170726 G A NA 0.2 0 0 MO 1031 MUC16 p.S5280L 19 9071607 G A NA 0.2 0 0.02 MO 1031 C11orf41 p.T465I 11 33565394 C T NA 0.1 0 0.32 MO 1031 SAMD13 p.L92F 1 84815382 G C NA 0.1 0 0 MO 1031 GLT1D1 p.E42Q 12 129360514 G C NA 0.1 0 0.05 MO 1031 PKD1L1 p.S2552T 7 47849102 C G NA 0.1 0 0.15 MO 1031 C6 p.Q111K 5 41199984 G T NA 0.1 0 0 MO 1031 BCL2L14 p.S92C 12 12232514 C G NA 0.1 0 0 MO 1031 RYR2 p.L192M 1 237540733 T A NA 0.1 0 0 MO 1031 NPAS3 p.L831I 14 34270100 C A NA 0.1 3 0.09 MO 1031 UGT8 p.D345E 4 115586905 C G NA 0.1 0 0 MO 1031 IGFN1 p.D1266H 1 201177817 G C NA 0.1 0 MO 1031 NCR3LG1 p.E23X 11 17373583 G T NA 0.1 0 0.6 MO 1031 GGT2 splice donor 22 21581683 A G NA 0.1 0 MO 1031 SPANXN3 p.D90H X 142596802 C G NA 0.1 0 0.01 MO 1031 CACNA1A p.D1411N 19 13372295 C T NA 0.1 0 0 MO 1031 UNC79 p.S1899X 14 94097168 C A NA 0.1 0 0 MO 1031 APOB p.E3545K 2 21229107 C T NA 0.1 0 0.07 MO 1031 CECR2 p.S1 

 05W 22 18028057 C G NA 0.1 0 0.02 MO 1031 CACNA1F p.R402Q X 49083503 C T NA 0.0 0 0.01 MO 1031 DUSP27 p.R551K 1 167096020 G A NA 0.0 1 0 MO 1031 ZNF831 p.P659L 20 57768050 C T NA 0.0 0 0.01 MO 1031 AC007431.1.1 p.G30A 17 55822545 C G NA 0.0 0 MO 1031 LEKR1 p.E87Q 3 156570767 G C NA 0.0 0 0.25 MO 1031 C2orf73 p.A139G 2 54586123 C G NA 0.0 0 0.2 MO 1031 CACNA1E p.A1489T 1 181727218 G A NA 0.0 0 0.04 MO 1031 NRAP p.E1274D 10 115365614 C A NA 0.0 0 0.07 MO 1031 SLC10A1 p.S206C 14 70246028 G C NA 0.0 0 0.01 MO 1031 PDZD3 p.S356L 11 119059398 C T NA 0.0 1 0.03 MO 1031 DMRTA2 splice a 

 c. 1 50885407 C T NA 0.0 0 MO 1031 ALPPL2 p.L273M 2 233273244 C A NA 0.0 0 0.3 MO 1031 DDI1 p.E395Q 11 103908733 G C NA 0.0 0 0.25 MO 1031 TRDN p.D275H 6 123818368 C G NA 0.0 0 0 MO 1031 C10orf71 p.L9 

 0P 10 50533529 T C NA 0.0 0 0.23 MO 1031 GRP142 p.G311S 17 72368281 G A NA 0.0 1 0.03 MO 1031 GRP142 p.E452Q 17 72368704 G C NA 0.0 0 0.13 MO 1031 CCDC27 p.E391K 1 3679888 G A NA 0.0 0 MO 1031 DCDC2C p.I77M 2 3774595 C G NA 0.0 0 0.01 MO 1031 COL6A5 p.R1936W 3 130158438 C T NA 0.0 0 MO 1031 GHSR p.Q299E 3 172163157 G C NA 0.0 0 0.27 MO 1031 HTR1A p.R297Q 5 63256657 C T NA 0.0 0 0.33 MO 1031 GGNBP1 p.E102K 6 33556777 G A NA 0.0 0 0 MO 1031 SLC22A2 p.E93Q 6 160679513 C G NA 0.0 0 0.06 MO 1031 OR13C5 p.L9 

 M 9 107361490 A T NA 0.0 0 0.15 MO 1031 OR52I2 p.S260L 11 4608821 C T NA 0.0 0 0 MO 1031 KRT76 p.F269L 12 53169180 G C NA 0.0 0 0.1 MO 1031 CYP1A1 p.P82T 15 75015195 G T NA 0.0 0 0 MO 1031 FAM46 

  p.M388I X 79699202 G C NA 0.0 0 0.04 MO 1031 RBMXL3 p.P321L X 114424966 C T NA 0.0 0 MO 1051 CTNNA1 p.D814N 5 138268583 G A NO 146.0 0 0.18 MO 1051 TOP1 p.E289K 20 39726867 G A NO 45.1 0 0.26 MO 1051 TOP1 p.K321N 20 39726965 G C NO 45.1 0 0 MO 1051 MAP4 p.E327Q 3 47933003 C G NO 41.3 0 0.03 MO 1051 TP53 p.G199E 17 7578253 C T NO 18.3 37 0 MO 1051 ESR1 p.Y537S 6 152419923 A C NO 12.3 2 0 MO 1051 PTK2B p.E474K 8 27294717 G A NO 11.9 3 0.02 MO 1051 AR p.G21A X 66765050 G C NO 9.3 0 0 MO 1051 PTPRT p.S249L 20 41385215 G A NO 8.7 0 0.35 MO 1051 FYN p.R481Q 6 111983114 C T NO 8.6 0 0.17 MO 1051 IGF1R p.K560N 15 99456363 G C NO 4.9 0 0.08 MO 1051 FLT4 p.G723A 5 180048007 C G NO 4.4 0 0 MO 1051 KAT6A p.S378L 8 41834756 G A NO 3.3 1 0.01 MO 1051 CD22 p.A483T 19 25831981 G A NO 2.6 0 0.46 MO 1051 ETV2 p.S169L 19 36134362 C T NO 2.3 0 0 MO 1051 PIK3CA p.H1047R 3 178952085 A G YES 2.1 1928 0.06 MO 1051 MYBL1 p.E593K 8 67479179 C T NO 1.2 0 0.15 MO 1051 BRIP1 p.Q1151K 17 59760956 C T NO 0.5 0 0 MO 1051 MAML2 p.Q553X 11 95825538 G A NO 0.4 0 1 MO 1051 POU6F2 p.G159K 7 39247183-4 GG AA NO 0.0 0 0 MO 1051 ALK p.E802K 2 29456514 C T NO 0.0 0 0.04 MO 1051 RPS25 p.K7N 11 118888746 C G NO 407.3 0 0.06 MO 1051 TUBA1B p.L70F 12 49523299 C G NO 327.2 0 0 MO 1051 IL32 p.D172G 16 3119304 A G YES 211.6 0 0 MO 1051 QARS p.F268L 3 49138860 G C NO 155.9 0 0 MO 1051 B4GALT3 p.G167E 1 161143829 C T NO 155.8 0 1 MO 1051 SF1 p.H415 

  11 64535140 G C NO 154.1 0 0 MO 1051 GANAB p.D434N 11 62398159 C T NO 131.0 0 0 MO 1051 PLXNB1 p.E1309K 3 48456626 C T NO 121.3 1 0.09 MO 1051 EFHD1 p.A70V 2 233498623 C T NO 109.5 0 0.23 MO 1051 DYNC1H1 p.E1284K 14 102466371 G A NO 90.4 0 0 MO 1051 PLEKHA6 p.E527K 1 204219688 C T NO 84.1 0 0 MO 1051 NTN4 p.V258I 12 96131736 C T NO 84.0 0 0.43 MO 1051 A1BG p.S95L 19 58864350 G A YES 83.4 0 0.73 MO 1051 SEC16A p. 

 2332E 9 139338286 G C NO 81.6 0 0.01 MO 1051 SDR39U1 p.G13V 14 24909758 C A NO 77.5 0 MO 1051 ZFAND6 p.S 

 7F 15 80414144 C T YES 70.5 0 0.01 MO 1051 HDAC7 p.R277W 12 48189511 G A NO 68.5 0 0 MO 1051 TMEM214 p.S552F 2 27267930 C T NO 62.7 0 0 MO 1051 LUC7L2 p.D85H 7 139083441 G C NO 58.9 0 0 MO 1051 PIN1 p.V55I 19 9949216 G A NO 51.5 0 0.3 MO 1051 ZNF296 p.K279N 19 45575450 C G NO 51.2 0 0.01 MO 1051 ZNF296 p.W170X 19 45575777 C T NO 51.2 0 0.42 MO 1051 MHRN1 p.P27Q 16 4675041 C A NO 46.3 0 0 MO 1051 NBPF10 p.L92F 1 14529 

 21 C T YES 46.3 0 0.02 MO 1051 COMTD1 p.R42Q 10 76995471 C T NO 45.4 0 0.65 MO 1051 SLC15A3 p.S358C 11 60709541 G C NO 43.2 0 0.01 MO 1051 DAG1 p.F692L 3 49570020 C G NO 40.2 0 0.45 MO 1051 DAG1 p.F791L 3 49570317 C A NO 40.2 0 0 MO 1051 DAG1 p.L 

 19V 3 49570399 C G NO 40.2 0 0.07 MO 1051 DAG1 p. 

 864K 3 49570534 C A NO 40.2 0 0.12 MO 1051 COPB1 p.D320N 11 14502643 C T NO 37.8 0 0.01 MO 1051 HIST2H2BE p.E114K 1 149857851 C T NO 34.4 1 MO 1051 MSMO1 p.H250Y 4 1662629 

 4 C T NO 33.7 0 0 MO 1051 SLC38A10 p.E519Q 17 79226385 C G NO 33.6 0 0 MO 1051 SLC35B1 p.S321Y 17 47780285 G T NO 33.5 0 0 MO 1051 PSMD1 p.G285D 2 231937102 G A NO 30.2 0 0.4 MO 1051 NACC1 p.R298W 19 13246913 C T YES 30.1 0 0.02 MO 1051 ZFP36L2 p. 

 139X 2 43452528 G A NO 30.0 0 0.32 MO 1051 THBS2 p.H201Y 6 169648520 G A NO 29.8 0 0.05 MO 1051 CHD1 p. 

 93E 5 96218833 G C NO 29.1 0 0 MO 1051 SK 

  p.S515C 1 2235801 C G NO 27.0 0 0.3 MO 1051 DHX30 p.E368K 3 47887268 G A NO 26.9 1 0.02 MO 1051 FCGR3A p.F212V 1 161514542 A C NO 26.7 0 0.24 MO 1051 GRSF1 p.R42C 4 71705097 G A NO 26.7 0 MO 1051 RAVER1 p.E642K 19 10429021 C T NO 25.8 0 0.33 MO 1051 TRIM26 p.E391Q 6 30154102 C G NO 25.2 0 0.09 MO 1051 LSS p.A 

 93S 21 47611140 C A NO 25.0 0 0.54 MO 1051 NBPF12 p.E84Q 1 146397433 G C NO 24.7 0 0 MO 1051 NBPF12 p.E50Q 1 146398387 G C NO 24.7 0 1 MO 1051 BRAT1 p.S274F 7 2582940 G A NO 23.9 0 0.7 MO 1051 USP22 p.S307L 17 20916167 G A NO 23.3 0 0 MO 1051 FAM208A p.D824E 3 56675524 G C NO 22.7 0 0.63 MO 1051 DYRK1A p.S258C 21 38862585 C G NO 22.6 0 0 MO 1051 CEP104 p.E160K 1 3761864 C T NO 22.5 0 0.33 MO 1051 SHROOM3 p.Q331X 4 77660317 C T NO 21.8 0 0.36 MO 1051 MAN2A1 p.E1030K 5 109190952 G A NO 21.5 0 0.84 MO 1051 LFNG p.F350L 7 2566532 C G NO 21.1 0 0 MO 1051 CC2D1A p.E772Q 19 14038076 G C NO 20.4 0 0.01 MO 1051 ZNF213 p.K355X 16 3191031 C T NO 20.2 0 0.04 MO 1051 LRPPRC p.R799T 2 44170934 C G NO 20.1 0 0.02 MO 1051 ANKRD30A p.E1234K 10 37508508 G A NO 20.0 0 0.05 MO 1051 NUP205 p.S1666I 7 135315156 G T YES 19.7 0 0.01 MO 1051 RAP1GAP p.S525C 1 21929351 G C NO 19.4 0 0 MO 1051 KLHL17 p.E159K 1 897116 G A NO 19.4 0 0 MO 1051 HTATSF1 p.D669H X 135593909 G C NO 19.4 0 0 MO 1051 GBP2 p.9174A 1 8 

 583365 G C NO 19.2 0 0 MO 1051 BAZ1A p.D639H 14 352530 

 0 C G NO 19.0 0 0 MO 1051 ABCG1 p.E191K 21 43697038 G A NO 18.8 0 0.31 MO 1051 TRIM41 p.F425L 5 180660747 C G NO 18.6 0 0.1 MO 1051 TRAPPC4 p.S132L 11 118890904 C T NO 17.5 0 0.1 MO 1051 GAS6 p.E385X 13 114531675 C A NO 17.1 0 0.01 MO 1051 ITSN1 p.E686K 21 35169786 G A NO 16.3 0 0 MO 1051 CD52 p.G43E 1 26646735 G A NO 15.9 0 0.12 MO 1051 HEXDC p.A413S 17 80399749 C T NO 15.3 0 MO 1051 NT5DC1 p.L21V 6 116422154 C G NO 15.1 0 0.73 MO 1051 GATAD2B p.M107I 1 153800503 C G NO 15.1 0 0.01 MO 1051 USP48 p.D893N 1 22028041 C T NO 14.9 0 0 MO 1051 USP48 p.E858K 1 22030055 C T NO 14.9 0 0.01 MO 1051 SIN3A p.R1263C 15 75664355 G A NO 14.6 0 0.23 MO 1051 PLEKHG 

  p.Q473H 1 6530918 C G NO 14.3 0 0 MO 1051 CCDC57 p.E754K 17 80086458 C T NO 14.1 0 0.06 MO 1051 POLR2B p.K497N 4 57876613 A C NO 14.0 0 0 MO 1051 HOXB7 p.T163A 17 46685371 T C NO 13.2 0 0 MO 1051 NOTCH2NL p.S67P 1 145273345 T C NO 13.2 0 0 MO 1051 PCMTD1 p.R335T 8 52732981 C G NO 13.1 0 0.4 MO 1051 MRPS18C p.P133S 4 84382318 C T NO 13.1 0 0 MO 1051 GMNN p.D204N 6 24786007 G A NO 12.9 0 0 MO 1051 GTPBP3 p.R14H 19 17448461 G A NO 12.8 0 MO 1051 NOL8 p.E759K 9 95076632 C T NO 12.7 0 0.1 MO 1051 IMPAD1 p.S244F 8 57878827 G A NO 11.7 0 0.01 MO 1051 VPS13C p.E3613K 15 62160884 C T NO 11.6 0 0 MO 1051 USP36 p.E484K 17 76803676 C T NO 11.4 0 0.02 MO 1051 ZNF646 p.D551N 16 31089296 G A NO 11.4 1 0.71 MO 1051 ZKSCAN1 p.E320Q 7 99631086 G C NO 11.4 0 0.15 MO 1051 MANBA p.E697Q 4 103557090 C G NO 11.2 0 0.01 MO 1051 FAM8A1 p.E94Q 6 17600920 G C NO 11.0 1 0.1 MO 1051 SENP3 p.D337H 17 7468329 G C NO 10.9 0 0 MO 1051 YLPM1 p.D377H 14 75247126 G C NO 10.8 2 0 MO 1051 TBC1D7 p.S292L 6 13305340 G A NO 10.7 0 0 MO 1051 CDRT4 p.S80C 17 15341307 G C NO 10.0 0 0.07 MO 1051 DDX19A p.E299X 16 70400639 G T NO 9.7 0 0 MO 1051 ZNF747 p.L16V 16 30545955 G C NO 9.5 0 0.06 MO 1051 C12orf35 p.M1479I 12 32138326 G A NO 9.5 0 0.52 MO 1051 DHX29 p.E1180Q 5 54558748 C G NO 9.2 0 0.64 MO 1051 HIVEP1 p.S1864F 6 12125619 C T NO 8.4 0 0.05 MO 1051 HDAC5 p.W792L 17 42161001 C A NO 8.3 0 0 MO 1051 C5orf51 p.E28K 5 41904551 G A NO 7.7 0 0.03 MO 1051 C1orf54 p.D110H 1 150253273 G C NO 7.7 0 0.05 MO 1051 AFF4 p.L723F 5 150253273 C G NO 7.6 0 0 MO 1051 NUFIP2 p.L644F 17 132232153 C G NO 7.6 0 0.26 MO 1051 NUFIP2 p.G331R 17 27613080 C G NO 7.6 0 0 MO 1051 NUFIP2 p.A305S 17 27614021 C A NO 7.6 0 0 MO 1051 NUFIP2 p.T259P 17 27614237 C G NO 7.6 0 0.03 MO 1051 CCDC25 p.E193K 8 27598009 C T NO 7.6 0 0.05 MO 1051 MASP1 p.F113L 3 186980407 G C NO 7.2 0 0.13 MO 1051 MCM2 p.E235K 3 127324990 G A NO 6.7 0 0.79 MO 1051 DNAH14 p.E3150Q 1 225519142 G C NO 6.8 0 0.17 MO 1051 DNAH14 p.E3166K 1 225519190 G A NO 6.8 0 0.02 MO 1051 GPATCH8 p.D875N 17 42476822 C T NO 6.6 0 0.95 MO 1051 PAPD5 p.E547K 16 50259080 G A NO 6.6 0 0.08 MO 1051 PCNXL2 p.I1505T 1 233160983 A G NO 6.1 0 0 MO 1051 PANX1 p.F15L 11 93862523 C G NO 6.1 0 0.25 MO 1051 KIAA1731 p.K2N 11 93399879 G C NO 5.7 0 0.01 MO 1051 FAM83D p.E36K 20 37555101 G A NO 5.4 0 0.03 MO 1051 FAM83D p.D93N 20 37555272 G A NO 5.4 0 0.09 MO 1051 MAP4K4 p.R1045Q 2 102493549 G A NO 5.4 0 0 MO 1051 LYST p.L2316V 1 235920694 G C NO 5.4 0 0.24 MO 1051 CYP4F2 p.E328Q 19 15997055 C G NO 5.2 0 0.07 MO 1051 AVIL p.E304Q 12 58203409 C G NO 5.2 0 0 MO 1051 HSPA13 p.S304C 21 15746443 G C NO 5.1 0 0 MO 1051 TRMT12 p.E391K 8 125464339 G A NO 5.0 0 0.13 MO 1051 PPP1R12B p.S516L 1 202411580 C T NO 4.9 0 0.02 MO 1051 GTF2E1 p.E389K 3 120500162 G A NO 4.8 0 0.07 MO 1051 PGLTRP2 p.R430H 19 15582755 C T YES 4.7 0 0 MO 1051 NFATC1 p.E917K 18 77287533 G A NO 4.5 0 0 MO 1051 CD97 p.F645L 19 14517256 C G NO 4.3 0 0.04 MO 1051 HELQ p.D771H 4 84350884 C G NO 4.1 0 0.1 MO 1051 RANBP6 p.L818F 9 6013154 C G NO 4.1 0 0.03 MO 1051 CCDC99 p.E213K 5 169021254 G A NO 3.9 0 0.01 MO 1051 C2orf126 p.G 

 2E 2 200776346 G A NO 3.8 0 0 MO 1051 C14orf126 p.E167K 14 31917343 C T NO 3.6 0 0.02 MO 1051 TTC3 

 A p.E518K 2 178481878 C T NO 3.5 0 0 MO 1051 FBXL7 p.E314K 5 15936759 G A NO 3.3 0 0.07 MO 1051 ZNF770 p.A140T 15 35275218 C T YES 3.0 0 0.24 MO 1051 XDH p.R943W 2 31572694 G A YES 2.9 0 0.01 MO 1051 OBSCN p.E4760K 1 228506731 G A NO 2.9 0 0 MO 1051 C2orf67 p.S519L 2 210940475 G A NO 2.7 0 0.03 MO 1051 C2orf15 splice a 

 c. 3 119427437 G C NO 2.7 0 MO 1051 PPTC7 p.D78N 12 110989765 C T NO 2.7 0 0 MO 1051 DOCK10 p.E1140Q 2 225672795 C G NO 2.7 0 0.01 MO 1051 E 

 DR1 p.D291H 7 37989834 G C NO 2.5 0 0.07 MO 1051 SEMA5B p.E768Q 3 122632250 C G NO 2.5 0 0.51 MO 1051 FSIP2 p.E6754K 2 186678437 G A NO 2.5 0 0.01 MO 1051 KIAA0753 splice a 

 c. 17 6528182 C T NO 2.4 0 MO 1051 INTS2 p.E368Q 17 59984872 C G NO 2.3 0 0.49 MO 1051 KIAA1549 p.P196A 7 138603636 G C NO 2.3 0 0 MO 1051 FGD6 p.E1422Q 12 95475325 C G NO 2.2 0 0.02 MO 1051 FAM22D p.H35Y 10 89118125 C T NO 2.0 0 0.42 MO 1051 ZNF546 p.S570X 19 40520886 C G NO 1.9 0 0.29 MO 1051 MAP1B p.E678Q 5 71491214 G C NO 1.8 1 0.04 MO 1051 SRR p.G192V 17 2224891 G T NO 1.7 0 0 MO 1051 ELOVL2 p.L235H 6 1098997 A T NO 1.6 0 0.17 MO 1051 FJX1 p.D291H 11 35641055 G C NO 1.6 0 0 MO 1051 FEZ1 p.E190Q 11 125330493 C G NO 1.4 0 0.03 MO 1051 P2RX7 p.V475I 12 121622240 G A YES 1.4 0 0.17 MO 1051 KIAA1524 p.E785K 3 108272549 C T NO 1.2 0 0.18 MO 1051 GRIN2D p.E815X 19 48945409 G T NO 1.2 0 0.1 MO 1051 ATOH8 p.S209L 2 85981938 C T NO 1.1 0 0.02 MO 1051 KIF21B p.L1373F 1 200948667 G A NO 0.9 0 MO 1051 ABCA10 p.G557E 17 67189361 C T NO 0.9 0 0 MO 1051 PLXNA4 p.V591I 7 131912321 C T YES 0.8 0 0.25 MO 1051 ST 

 SIA4 p.M134I 5 100222148 C T NO 0.7 0 0.01 MO 1051 DNAH7 p.E554K 2 196851884 C T NO 0.6 0 0.29 MO 1051 FAM124B p.S398C 2 225244465 G C NO 0.5 0 0.01 MO 1051 LINGO4 p.P524S 1 151773611 G A YES 0.5 0 0.02 MO 1051 PNMA3 p.E189K X 152225977 G A NO 0.4 0 0.01 MO 1051 AKR1E2 p.S126X 10 4877919 C A NO 0.4 0 0.04 MO 1051 SHANK1 p.S212L 19 51217444 G A NO 0.4 0 0 MO 1051 C9orf153 p.R73T 9 88842794 C G NO 0.3 0 0.05 MO 1051 FCAMR p.R18K 1 207140983 C T NO 0.3 0 0 MO 1051 CDH7 p.D288N 18 63491948 G A NO 0.3 0 0.01 MO 1051 FHOD3 p.K788N 18 34298150 G C NO 0.2 0 0.04 MO 1051 CUBN p.H2474Y 10 16955923 G A NO 0.2 0 0.01 MO 1051 PHOSPHO1 p.E117Q 17 47302063 C G NO 0.2 0 0.03 MO 1051 FBXO15 p.R297C 18 71790624 G A YES 0.2 2 0 MO 1051 CCDC36 p.Q272X 3 49293744 C T NO 0.2 0 0 MO 1051 FAT4 p.Q760X 4 126239844 C T NO 0.2 0 0.81 MO 1051 FAT4 p.S1870C 4 126329638 C G NO 0.2 0 0.06 MO 1051 ADCY10 p.R109Q 1 167871010 C T NO 0.2 1 0.42 MO 1051 FBXL13 p.M68I 7 102695601 C T NO 0.2 0 0.24 MO 1051 DNAH6 p.D2485Y 2 84921533 G T NO 0.2 0 0 MO 1051 PAPPA2 p.R1488C 1 175738881 C T NO 0.2 0 0 MO 1051 PI16 splice a 

 c. 6 36926920 G A NO 0.1 0 MO 1051 KIRREL2 p.L684V 19 36357317 C G NO 0.1 0 0.16 MO 1051 CR1 p.Q572H 1 207726161 G T YES 0.1 0 0.04 MO 1051 C9orf131 p.Q171E 9 35043137 C G NO 0.1 0 0 MO 1051 ZPLD1 p.S375F 3 102196290 C T NO 0.1 0 0.01 MO 1051 HOXA2 p.Q252X 7 27140722 G A NO 0.1 0 0.07 MO 1051 EYS p.I3056M 6 64430759 G C NO 0.1 0 0 MO 1051 BNC1 p.G596A 15 83932216 C G NO 0.1 0 0.43 MO 1051 TYRP1 p.E525K 9 12709141 G A NO 0.1 0 0.01 MO 1051 GCK p.E246K 7 44187379 C T NO 0.0 0 0.01 MO 1051 FCRLA p.E156K 1 161681957 G A NO 0.0 0 0.02 MO 1051 CNKSR2 p.G368E X 21549985 G A NO 0.0 0 0.05 MO 1051 ODZ1 p.M1531I X 123554529 C T NO 0.0 0 0.34 MO 1051 MYT1L p.P351S 2 1926490 G A NO 0.0 0 0.48 MO 1051 TTN p.E4790Q 2 179500735 C G NO 0.0 0 MO 1051 TTN p.R3402K 2 179621465 C T NO 0.0 0 MO 1051 RPH3A p.D676H 12 113334526 G C NO 0.0 0 0 MO 1051 MUC2 p.G305S 11 1079696 G A YES 0.0 0 0.88 MO 1051 FOXI2 p.P14L 10 129535578 C T NO 0.0 0 0.11 MO 1051 GABRR1 p.E432K 6 89888635 C T NO 0.0 1 0.09 MO 1051 RHAG p.Q104K 6 49586923 G T NO 0.0 0 0.21 MO 1051 LRRTM4 p.D54Y 2 77746835 C A NO 0.0 0 0 MO 1051 ADGB p.L1592F 6 147123105 G C NO 0.0 0 0.18 MO 1051 LEKR1 p.E12K 3 156 

 47152 G A NO 0.0 0 0.18 MO 1051 A2ML1 p.L1319F 12 9020847 C T NO 0.0 0 0.19 MO 1051 ATP12A p.L 

 98V 13 25283895 C G NO 0.0 0 0.01 MO 1051 SI p.D1389H 3 164727081 C G NO 0.0 0 0 MO 1051 CACNA1E p.R3C 1 181452887 C T NO 0.0 0 0 MO 1051 CBLN4 p.H125Y 20 54575822 G A NO 0.0 0 0 MO 1051 NKX2-3 p.D234H 10 1012950 

 3 G C NO 0.0 0 0 MO 1051 CIB4 p.E16Q 2 26864137 C G NO 0.0 1 0.02 MO 1051 OR5K3 p.R259X 3 98110284 C T NO 0.0 0 1 MO 1051 C9orf135 splice a 

 c. 9 72471470 G C NO 0.0 0 MO 1051 SLC1A6 p.F52L 19 15083567 G C NO 0.0 0 0.03 MO 1051 SPINT4 p.R65I 20 44352597 G T NO 0.0 0 0.09 MO 1069 ESR1 p.D538G 6 152419926 A G NO 60.5 2 0 MO 1069 ARID1B p.D2175G 6 157528853 A G NO 7.9 0 0.01 MO 1069 MTOR p.R281H 1 11308150 C T YES 5.5 1 0.01 MO 1069 ARID2 p.E245X 12 46230399 G T NO 5.4 0 0.04 MO 1069 FANCD2 p.Q1100E 3 10127569 C G NO 5.1 0 1 MO 1069 MUC16 p.S2675L 19 9083791 G A NO 154.6 0 0.06 MO 1069 UBA1 p.N928I X 47072525 A T NO 140.5 0 0 MO 1069 RPS6KB2 p.V48L 11 67196613 G T YES 72.6 0 0.08 MO 1069 C11orf80 p.A5 

 2T 11 66605913 G A NO 58.7 0 0 MO 1069 MOGS p.A470D 2 74689507 G T YES 38.1 0 0.03 MO 1069 CDR2L p.E193X 17 72999345 G T NO 36.9 0 0.06 MO 1069 TBC1D9B p.V43M 5 179331804 C T NO 34.8 0 0.01 MO 1069 HCFC1R1 p.R46L 16 3073490 C A NO 32.1 0 0.35 MO 1069 UBE2A p.T69I X 118716605 C T YES 29.2 0 0.84 MO 1069 CCDC88C p.Q1770R 14 91739747 T C NO 29.0 0 0.53 MO 1069 CASKIN2 p.S557I 17 73499750 C A NO 27.6 0 0 MO 1069 MBD3 p.F138L 19 1582706 G C NO 27.0 0 0.01 MO 1069 ACBD3 p.D392Y 1 226340237 C A NO 22.1 0 MO 1069 PDE4DIP p.K223Q 1 144923791 T G NO 20.0 0 0.09 MO 1069 CENPF p.E1583Q 1 214816428 G C NO 18.4 0 MO 1069 CENPF p.S1589R 1 214816446 A C NO 18.4 0 MO 1069 TNC p.V708E 9 117846496 A T NO 17.3 0 0 MO 1069 CCDC9 p.G459R 19 47774714 G A NO 16.3 1 0.69 MO 1069 NFRKB p.R184W 11 129755459 G A NO 13.7 0 0.02 MO 1069 KIAA1683 p.P36S 19 18378244 G A YES 12.1 0 0 MO 1069 CTSC p.L16F 11 88070795 G A YES 12.0 0 0.09 MO 1069 DUSP10 p.Y31S 1 221912995 T G NO 10.0 0 0 MO 1069 C15orf39 p.R824X 15 75500859 C T NO 8.7 0 0.03 MO 1069 ITGAX p.C108G 16 31368577 T G NO 8.7 0 0 MO 1069 FAM8A1 p.S147F 6 17601080 C T YES 8.4 0 0.03 MO 1069 NLGN2 p.R642Q 17 7320535 G A NO 6.7 0 MO 1069 PLS1 p.R274Q 3 142403170 G A NO 6.5 0 0.01 MO 1069 TTI2 p.H23Y 8 33370065 G A YES 6.1 0 0.15 MO 1069 PHF20L1 p.A95P 8 133807006 G C YES 5.5 0 0 MO 1069 ATRN p.H427Y 20 3541384 C T YES 4.6 0 0.13 MO 1069 DIEXF p.S246L 1 210010231 C T YES 4.3 0 0.31 MO 1069 UHRF2 splice domor 9 6493933 G A NO 3.9 0 MO 1069 EFCAB7 p.D269N 1 64011587 G A YES 3.3 0 0.02 MO 1069 TTC27 UNKNOWN 2 32991568 G C NO 2.9 0 MO 1069 KLHL24 p.I52V 3 183368298 A G NO 2.6 0 0.17 MO 1069 SHPRH p.E1228A 6 146243847 T G NO 2.6 0 0.08 MO 1069 PTPLAD2 p.V119I 9 21015925 C T NO 2.2 0 0.76 MO 1069 RFX7 p.Q703H 15 56387526 T G NO 1.4 0 0 MO 1069 C7orf60 p.G7D 7 112579786 C T YES 1.1 0 0 MO 1069 ADAMTS7 p.V49A 15 79092844 A G NO 1.0 0 0.04 MO 1069 FAM227A p.R369X 22 39003415 G A NO 0.9 0 1 MO 1069 CDC14A p.R236H 1 100928306 G A NO 0.7 0 0 MO 1069 CHST2 p.P284A 3 142840508 C G NO 0.5 0 0.27 MO 1069 ADAMTSL1 p.R1093C 9 18777504 C T YES 0.5 0 0.01 MO 1069 MCTF2 p.K356Q 15 95020020 A C YES 0.5 0 0.02 MO 1069 MAPTA p.V1155I 15 43817134 G A NO 0.5 0 0.06 MO 1069 PRDM8 p.A395T 4 81123799 G A YES 0.2 0 0.17 MO 1069 ANKRD1 p.G209A 10 92675953 C G NO 0.1 0 0 MO 1069 ZNF469 p.G694V 16 88495959 G T NO 0.1 0 0.02 MO 1069 C18orf34 p.L444F 18 30846957 C G NO 0.1 0 0.08 MO 1069 PAPPA2 p.P960L 1 176668368 C T YES 0.1 0 0 MO 1069 HOXD10 p.E227Q 2 176982240 G C NO 0.1 0 0.09 MO 1069 SCN3A p.F1177V 2 165970466 C C NO 0.1 0 0.05 MO 1069 PDIA2 p.W417C 16 336564 G T YES 0.0 0 0 MO 1069 SHISA6 p.F128V 17 11145121 T G NO 0.0 0 0 MO 1069 KIAA1549L p.E1244A 11 33612838 A C NO 0.0 0 0.01 MO 1069 ATP 

 A2 splice a 

 . 13 26043114 G T NO 0.0 0 MO 1069 LRRN4 p.A82V 20 6033201 G A NO 0.0 0 0.18 MO 1069 ABCD2 p.D737H 12 3994772 

  C G NO 0.0 0 0.01 MO 1069 FAT3 p.T2716A 11 92534325 A G NO 0.0 0 0.18 MO 1069 BTNL8 p. 

 426X 5 180377317 C T NO 0.0 0 1 MO 1069 LRRC7 p.S1063I 1 70504809 G T YES 0.0 1 0 MO 1069 PLA2G1B p.Y133X 12 120760044 A T NO 0.0 0 MO 1069 HMX1 p.V215O 4  

 69822 A T NO 0.0 0 0 MO 1069 AKR1B10 p.S305C 7 134225804 C G NO 0.0 0 0.05 MO 1069 SLC18A3 p.A180V 10 50819325 C T NO 0.0 0 0.38 MO 1069 OGDHL p.I517F 10 50953470 T A NO 0.0 0 0 MO 1069 OR4C16 p.G106R 11 55339919 G C NO 0.0 0 0.01 MO 1069 OR10G4 p.A90T 11 123886549 G A NO 0.0 0 0.79 MO 1129 ESR1 p.Y537S 6 152419923 A C NO 76.4 2 0 MO 1129 DEK p.A18T 6 18264167 C T YES 22.8 0 0.02 MO 1129 PIK3CA p.E542K 3 1789360 

 2 G A YES 4.3 603 0.04 MO 1129 ELK4 p.L412V 1 205585736 G C NO 4.2 0 MO 1129 MLL p.G1181V 11 118348889 G T NO 3.6 0 0 MO 1129 MAP3K5 p.C200Y 6 137026261 C T NO 0.7 0 0.05 MO 1129 WDR1 p.A239S 4 10089919 C A NO 105.9 0 0.13 MO 1129 TRIO splice donor 5 14359641 G A NO 82.4 0 MO 1129 SPEG p.G397S 2 220313069 G A NO 37.1 0 0.07 MO 1129 USP5 p.E29Q 12 6961428 G C NO 30.2 0 0 MO 1129 HEATR2 p.A666V 7 813750 C T YES 20.8 0 0.01 MO 1129 TUBB2A p.A248V 6 3154692 G A NO 10.6 0 0 MO 1129 CMAS p.V136I 12 22208391 G A YES 9.8 0 0.17 MO 1129 DHX8 p.Q317X 17 4157089 

  C T NO 6.5 0 0.01 MO 1129 ZP3 p.M289V 7 76069886 A G NO 5.8 0 0.29 MO 1129 ZP3 p.R294T 7 76069902 G C YES 5.8 0 0.25 MO 1129 ZCCHC6 p.S1170L 9 88924451 G A YES 5.4 0 0 MO 1129 ZPCS p.G194D 1 159558407 G A NO 4.4 0 MO 1129 CES1 p.S12A 16 55866934 A C NO 3.2 0 1 MO 1129 PRDM11 p.N201Y 11 45226274 A T YES 2.2 0 0.02 MO 1129 USP37 p.S968N 2 219319690 C T YES 2.1 0 0.41 MO 1129 DMD p.R1719H X 32381074 C T NO 1.2 0 0.05 MO 1129 HHATL p.R186H 3 42739770 C T NO 1.1 1 0 MO 1129 ODZ4 p.L1229F 11 78433828 G A NO 0.5 0 0 MO 1129 FAT4 p.L1006I 4 126240579 C A NO 0.5 0 0.19 MO 1129 ZFHX4 p.L2551M 8 7776680 

  C A NO 0.1 0 0.07 MO 1129 PABPC5 p.R169Q X 90691082 G A YES 0.1 1 0.01 MO 1129 ODZ1 p.S1848L X 123526026 G A NO 0.0 1 0.07 MO 1129 TMPRSS11F splice donor 4 68938039 A T NO 0.0 1 MO 1129 OR2J3 p.R17 

 C 6 29080190 C T YES 0.0 0 0.05 MO 1129 OR13C5 p.T160I 9 107361216 G A NO 0.0 0 0.05 MO 1129 OR1L4 p.W140R 9 125486686 T C NO 0.0 0 1 MO 1167 ESR1 p.D538G 6 152419926 A G NA 657.1 2 0 MO 1167 HLA-A p.G199R 6 29911296 G A NA 277.0 1 0 MO 1167 KIF1B p.E1506K 1 10425470 G A NA 24.5 0 0.08 MO 1167 DNMT3A p.E408A 2 25469545 T G NA 23.9 0 0.02 MO 1167 DNMT3A p.E426D 2 25469490 T G NA 23.9 0 0.13 MO 1167 RBMX p.R324P X 135956506 C G NA 11.2 0 0.05 MO 1167 MLXIP p.A518V 12 122618355 C T NA 164.9 0 0.24 MO 1167 MACF1 p.V1551G 1 39796897 T G NA 141.4 0 MO 1167 ATOX1 splicing 5 151138339 G A NA 138.2 0 MO 1167 CTDSP1 p.A69T 2 219266424 G A NA 133.1 0 0.6 MO 1167 HISTAH3H p.Q126X 6 27778227 C T NA 61.8 0 0.01 MO 1167 RAPGEF5 p.Y334N 7 22200203 A T NA 48.0 0 0.24 MO 1167 MLLT4 p.S1282F 6 168351879 C T NA 43.6 0 0 MO 1167 MEF2A p.Q428P 15 100252738 A C NA 34.6 3 0.23 MO 1167 LHFPL2 p.Y154H 5 77784947 A G NA 25.2 0 0 MO 1167 EDEM3 p.R253K 1 184692980 C T NA 22.7 0 0.08 MO 1167 EIF2C4 p.V154I 1 36291067 G A NA 20.5 0 0.59 MO 1167 RP3-402G11.5. 

  UNKNOWN 22 50639528 T C NA 18.3 0 MO 1167 ZFP91 p.C435F 11 58384770 G T NA 18.1 0 0 MO 1167 NBAS splicing 2 15613473 T G NA 16.8 0 MO 1167 NBAS p.T548I 2 15613428 G A NA 16.8 0 0.02 MO 1167 NBAS p.E535D 2 15613466 T G NA 16.8 0 0.77 MO 1167 ELL p.R424H 19 18561481 C T NA 12.9 0 0.3 MO 1167 KLHL26 p.D237H 19 18778917 A C NA 11.2 0 0.1 MO 1167 FDXR p.P3L 17 72869062 G A NA 9.6 0 0.1 MO 1167 SIRPA p.G109S 20 1895990 G A NA 6.7 0 1 MO 1167 SHROOM4 p.P9 

 S X 50381286 G A NA 6.0 0 0 MO 1167 SLC9A5 p.L836H 16 67304929 G A NA 5.6 0 0.19 MO 1167 UNC13D p.R1065X 19 73824126 G A NA 5.0 0 0.98 MO 1167 C22orf39 p.R29G 22 19435238 G C NA 2.6 0 0 MO 1167 ADRA1A p.T391M 8 26627895 G A NA 2.5 0 0 MO 1167 PLCE1 p.R435K 10 95892028 G A NA 2.5 0 0.18 MO 1167 ZFP91-CNTF p.C435F 11 58384770 G T NA 1.8 0 0 MO 1167 PCDHA10 p.A426V 5 140236910 C T NA 1.5 0 0.02 MO 1167 MUC4 p.A3654T 3 195507491 C T NA 1.4 0 MO 1167 IGFN1 p.G2022S 1 201180085 G A NA 0.8 0 MO 1167 ASPM p.V2717L 1 197070232 C G NA 0.8 0 0.04 MO 1167 BMP7 p.D410E 20 55746081 A T NA 0.7 0 0 MO 1167 B3GNT3 p.A286T 19 1792266 

  G A NA 0.3 1 0.05 MO 1167 DSG1 p.G535R 18 28919904 G A NA 0.1 0 MO 1167 CTSE p.R389H 1 206331145 G A NA 0.1 0 0 MO 1167 COL17A1 splicing 10 106800822 C T NA 0.1 0 MO 1167 IGHV4-31 p.P28S 14 10680 

 481 G A NA 0 0 0.02 MO 1167 IGHV4-31 p.V21L 14 106805502 C G NA 0 0 0.42 MO 1167 AC012414.1 p.T40K 15 21071492 G T NA 0 0 1 MO 1167 GABRA6 p.R48Q 5 161113340 G A NA 0 1 0 MO 1167 ADAM2 p.K349T 8 39627077 T G NA 0 0 0 MO 1167 FCER2 p.W167R 19 7755414 A T NA 0 0 0 MO 1185 ESR1 p.Y537S 6 152419923 A C NA 46.5 2 0 MO 1185 PTPRT p.S846F 20 40827900 G A NA 13.6 0 1 MO 1185 CDH1 p.S70F 16 68835618 C T NA 9.4 0 0 MO 1185 CDH1 p.Q641X 16 68856113 C T NA 9.4 0 0.24 MO 1185 LRP1B p.P3139T 2 141242922 G T NA 8.3 0 0.31 MO 1185 FGFR1 p.R840Q 8 38271189 C T NA 5.9 0 0.6 MO 1185 TERT p.V1035I 5 1255456 C T NA 0.1 0 0.57 MO 1185 ALK p.E1299K 2 29430080 C T NA 0.0 0 0 MO 1185 MUC5B p.S1632L 11 1262996 C T NA 1131.5 0 MO 1185 VIM p.E134K 10 17271821 G A NA 603.8 0 0 MO 1185 HNRNPK p.L6 

 F 9 86591921 G A NA 292.6 0 0.03 MO 1185 EIF5A p.Y157C 17 7214778 A G NA 135.4 0 0 MO 1185 HNRNPU p.S4L 1 245027599 G A NA 122.4 0 0 MO 1185 SCCPDH p.S84L 1 246890254 C T NA 98.6 0 0 MO 1185 TXNIP p.E165K 1 145440059 G A NA 79.5 0 0 MO 1185 INF2 p.E58K 14 105167874 G A NA 72.3 0 0.07 MO 1185 AHNAK p.P2833A 11 62293392 G C NA 64.9 0 0.07 MO 1185 ALYREF p.R151C 17 79847145 G A NA 50.1 0 0 MO 1185 RERE p.S10 

 4A 1 8420317 A C NA 40.3 0 0.32 MO 1185 MEPCE p.Q137X 7 100028050 C T NA 38.9 0 0.22 MO 1185 SSSCA1 p.S165Y 11 65339099 C A NA 32.2 0 0 MO 1185 TBCD p.P1143T 17 80895956 G A NA 30.6 0 0.06 MO 1185 STX16 p.D199N 20 57245606 G A NA 30.1 0 0.01 MO 1185 AGPAT6 P.Q278X 8 41470400 C T NA 27.2 0 0 MO 1185 RBM25 p.R433Q 14 73572710 G A NA 26.6 0 0.42 MO 1185 MUC16 p.R12975W 19 9010995 G A NA 24.6 0 0.01 MO 1185 ZFAND2B p.Q41X 2 220072114 C T NA 20.6 0 0.15 MO 1185 PRKAA1 p.R144H 5 40771943 C T NA 19.8 0 0 MO 1185 ITGAV p.T76P 2 187466788 A C NA 19.7 0 0 MO 1185 NFKBIZ p.M376I 3 101572498 G A NA 19.2 0 0.03 MO 1185 NOP14 splicing 4 2958396 C A NA 19.1 0 MO 1185 AP3B1 p.S31L 5 77590312 G A NA 18.2 1 0.03 MO 1185 SNTB1 p.G224D 8 121706049 C T NA 17.2 0 0.04 MO 1185 GGPS1 p.P210K 1 235505812 G A NA 16.1 0 0 MO 1185 SLC2A11 p.P203L 22 24219643 C T NA 14.4 0 0 MO 1185 KIAA0020 p.E353K 9 2824794 C T NA 12.7 0 MO 1185 RBBP6 p.A595T 16 24578657 G A NA 12.3 0 0.07 MO 1185 TMEM135 p.R421X 11 87032259 C T NA 12.2 1 1 MO 1185 STX18 p.T18M 4 4543639 G A NA 11.3 0 0.02 MO 1185 SBNO1 p.M208I 12 123825562 C T NA 10.7 0 0.87 MO 1185 NCF2 p.R38L 1 183559352 C A NA 10.2 0 0 MO 1185 ZNHIT2 p.Q366P 11 64884029 T G NA 9.6 0 0.01 MO 1185 EMR2 p.K154I 19 14877816 T A NA 8.4 0 0.22 MO 1185 SIRT6 p.R150X 19 4175924 G A NA 7.6 0 1 MO 1185 PASK p.V1217G 2 242047620 A C NA 7.3 0 0 MO 1185 TRIM32 p.P431T 9 119461312 C A NA 6.7 0 0 MO 1185 CENPF p.S1477X 1 214816111 C A NA 6.5 0 MO 1185 PLEKHG2 p.S663F 19 39913682 C T NA 5.6 0 0 MO 1185 ATP2B1 p.E1136K 12 89985018 C T NA 4.1 0 0.12 MO 1185 FKTN p.E456K 9 108397 

 25 G A NA 3.7 0 0.05 MO 1185 PCDHGB4 p.L212F 5 140768087 G C NA 3.2 0 MO 1185 WDFY4 p.F820I 10 49951565 T A NA 2.9 0 0.39 MO 1185 ZNF528 p.S144L 19 52918536 C T NA 2.9 0 1 MO 1185 KLF8 p.D65N X 56291724 G A NA 2.2 0 0.43 MO 1185 STX16-NPEPL1 p.D199N 20 57245606 G A NA 2.0 0 0.01 MO 1185 EVX1 p.Y317S 7 27285770 A C NA 2.0 0 MO 1185 AMPH p.E459K 7 38457448 C T NA 1.8 0 0.05 MO 1185 CCDC40 p.E991K 17 78064076 G A NA 1.4 0 0.04 MO 1185 CCDC40 p.R980Q 17 78064044 G A NA 1.4 0 0 MO 1185 SVEP1 p.S1470F 9 113208171 G A NA 1.3 0 0 MO 1185 PPFIA3 p.K1132N 19 49652845 G C NA 1.1 0 0 MO 1185 HOXD3 p.R422X 2 177036967 C T NA 1.0 0 1 MO 1185 DNAH10 p.A1831T 12 124332538 G A NA 0.9 0 0 MO 1185 SPTB p.E171K 14 65268999 C C NA 0.9 0 0 MO 1185 ZNF208 p.L34F 19 22171613 T g NA 0.5 0 0 MO 1185 KIRREL p.E460Q 1 158061205 G c NA 0.4 0 0.15 MO 1185 RIMS1 p.E1471Q 6 73100344 G C NA 0.3 0 0 MO 1185 OR4C3 p.W174X 11 48347014 G A NA 0.1 0 0 MO 1185 NR6A1 p.S17L 9 127533349 G A NA 0.1 0 0 MO 1185 LAMA1 p.K247N 18 7049104 T A NA 0.1 0 MO 1185 KCNN3 p.C519W 1 154705512 A C NA 0.1 0 0 MO 1185 HRNR p.R2466H 1 152186708 C T NA 0.0 0 0.59 MO 1185 KRT6C p.S227N 12 52865925 C T NA 0.0 0 0.26 MO 1185 IRX1 p.G300S 5 3599960 G A NA 0.0 0 0.38 MO 1185 PRH2 p.R119C 12 11083515 C T NA 0.0 0 0.07 MO 1185 LVRN.1 p.H813Y 5 115350211 C T NA 0.0 0 0.05 MO 1185 ALPK2 p.E144K 18 56203089 C T NA 0.0 0 0 MO 1185 UNC79 p.D496N 14 94007139 G A NA 0.0 0 0 MO 1185 UNC80 p.Q1837H 2 210791613 G C NA 0.0 0 0.34 MO 1185 GRIK3 p.E852Q 1 37270599 C G NA 0.0 0 0.58 MO 1185 TGM6 p.E408K 20 2384355 G A NA 0.0 0 1 MO 1185 HRG p.D170N 3 186389528 G A NA 0.0 0 0.69 MO 1185 GDA p.D155N 9 74825681 G A NA 0.0 0 0.01 MO 1185 OR10H1 p.E173D 19 15918329 C A NA 0.0 0 0.58 MO 1185 ZNF454 p.S398C 5 178392598 C G NA 0.0 0 0.04 MO 1185 OR2T27 p.Y120C 1 248813827 T C NA 0.0 0 0.02 MO 1185 IGHV4-31 p.V21L 14 106805502 C G NA 0.0 0 0.42 MO 1185 IGHV4-31 p.P28S 14 106805481 G A NA 0.0 0 0.02

indicates data missing or illegible when filed

TABLE 4 Case Loc Loc # Exon Adj Copy MiOncoSeq ID Chr Start End Targets Num Ratio Panel Genes MO_1031 4 68,588,132 68,829,154 24 10.35 MO_1031 10 17,130,256 17,432,516 45 8.28 MO_1031 10 81,316,935 84,498,366 95 8.26 NRG3 MO_1031 11 92,861,858 92,931,012 11 7.77 MO_1031 4 68,919,654 69,107,468 22 7.59 MO_1031 8 33,230,180 32,251,814 3 7.50 MO_1031 10 74,451,906 75,530,518 186 7.17 MO_1031 10 76,154,035 77,312,230 59 6.79 KAT6B MO_1031 11 69,456,232 70,196,120 71 6.75 CCND1, FADD, FGF19, FGF3, FGF4 MO_1031 8 35,401,916 38,599,900 236 6.74 BAG4, FGFR1, GPR124, LSM1, WHSC1L1, ZNF703 MO_1031 10 12,802,948 13,568,184 72 6.69 MO_1031 10 11,551,638 12,272,906 88 6.57 MO_1031 18 6,171,882 6,263,988 9 6.46 MO_1031 10 123,233,969 123,629,536 27 6.32 FGFR2 MO_1031 4 69,111,386 69,215,570 15 5.81 MO_1031 4 66,189,850 67,142,530 19 5.51 EPH45 MO_1031 10 75,532,834 76,074,464 88 5.15 MO_1031 10 77,542,720 81,266,457 158 5.13 MO_1031 8 39,442,183 41,164,370 74 4.72 MO_1031 6 38,602,921 39,142,362 94 4.76 MO_1031 11 90,288,976 92,718,066 35 4.61 MO_1031 3 87,275,319 88,205,533 26 4.11 MO_1031 18 2,539,035 6,138,182 201 4.03 MO_1031 10 11,505,120 11,543,156 8 3.99 MO_1031 12 3,982,470 4,481,740 14 3.94 CCND2, FGF23 MO_1031 18 6,301,996 11,825,000 204 3.92 MO_1031 12 13,093,751 13,154,594 9 3.86 MO_1031 10 17,495,666 17,686,317 7 3.75 MO_1031 16 70,526,211 74,442,070 6 3.36 MO_1031 10 12,277,132 12,767,372 12 3.23 MO_1031 8 33,310,878 36,093,272 29 3.19 MO_1031 18 61,747,550 66,368,940 38 3.15 MO_1031 12 21,919,132 22,837,826 94 3.09 MO_1031 11 70,200,412 71,850,892 187 3.06 MO_1031 11 76,706,811 77,825,721 158 3.03 PAK1 MO_1031 12 208,418 1,769,452 175 2.89 KDM5A, WNT5B MO_1031 12 4,488,584 5,154,919 75 2.88 FGF23, FGF6 MO_1031 11 78,497,956 79,113,172 14 2.70 MO_1031 18 11,851,800 15,004,215 220 2.70 MO_1031 4 54,853,144 54,967,958 7 2.67 CHIC2 MO_1031 17 51,901,464 81,083,588 3437 2.61 AATK, AXIN2, BIRC5, BRIP1, CD79B, GRB2, HLF, PPM1D, PRKAR1A, RAD51C, RNF213, RNF43, RPS6KB1, RPTOR, SRSF2, TMC6, TMC8 MO_1031 18 158,542 1,358,660 93 2.58 YES1 MO_1031 11 67,864,607 68,031,182 17 2.54 MO_1031 4 73,927,524 74,735,596 110 2.49 MO_1031 1 201,755,699 201,817,549 24 2.49 MO_1031 12 21,201,680 21,807,605 97 2.42 MO_1031 18 61,471,724 61,654,338 25 2.42 MO_1031 1 207,245,672 206,390,788 139 2.41 MO_1031 4 68,202,157 88,547,886 82 2.38 MO_1031 11 72,945,843 74,209,014 177 2.37 MO_1031 11 28,080,588 36,123,407 438 2.35 EHF, ELF5, LMO2, WT1 MO_1031 3 85,755,692 87,100,805 15 2.34 CADM2 MO_1031 8 32,406,234 32,621,669 18 2.31 NRG1 MO_1031 11 9,983,601 10,875,419 102 2.25 MO_1031 4 75,065,608 75,959,197 24 2.24 AREG, BTC, EPGN, EREG MO_1031 11 71,903,301 72,342,154 66 2.24 MO_1031 11 74,907,638 74,915,575 5 2.24 MO_1031 8 146,115,084 146,279,458 14 2.22 MO_1031 11 96,074,868 99,426,930 10 2.22 MAML2 MO_1031 4 69,313,202 70,826,694 84 1.99 MO_1031 1 190,067,665 193,218,926 72 1.99 CDC73 MO_1031 12 13,197,380 21,176,141 359 1.88 PIK3C2G MO_1031 18 59,894,692 61,468,169 142 1.87 BCL2, KDSR MO_1031 18 56,377,286 70,502,474 86 1.87 MO_1031 4 72,607,550 73,923,894 43 1.85 MO_1031 11 22,214,994 28,078,414 156 1.84 BDNF, FANCF MO_1031 12 23,688,112 26,985,695 156 1.82 KRAS MO_1031 8 66,617,076 141,931,000 2986 1.81 EXT1, HEY1, MTDH, MYBL1, MYC, NBN, NCOA2, PREX2, PTK2, PVT1, RSPO2, RUNX1T1, STK3, TRIB1, YWHAZ, ZNF704 MO_1031 16 29,820,892 29,842,221 10 1.81 MO_1031 4 52,709,311 54,442,468 99 1.80 MO_1031 1 172,108,064 184,537,648 925 1.80 ABL2, FASLG MO_1031 1 206,903,313 207,244,824 72 1.80 MO_1031 1 201,821,210 201,865,775 25 1.79 MO_1031 19 58,904,864 59,083,890 56 1.77 MO_1031 3 27,152,740 32,612,234 204 1.77 TGFBR2 MO_1031 14 50,044,532 56,150,882 590 1.75 CDKN3 MO_1031 12 133,728,390 133,770,132 7 1.75 MO_1031 11 75,708,074 76,701,540 86 1.73 C11orf30, WNT11 MO_1031 10 84,625,118 86,273,618 61 1.72 NRG3 MO_1031 12 5,541,438 13,068,862 1014 1.71 CDKN1B, ETV6, ING4, LRP6, NTF3, STYK1, ZNF384 MO_1031 1 209,602,742 210,856,990 100 1.71 IRF6 MO_1031 4 55,106,349 56,225,649 71 1.70 KDR, KIT, PDGFRA MO_1031 16 31,804,064 31,895,792 5 1.69 MO_1031 12 57,111,463 57,118,361 4 1.68 MO_1031 17 38,487,509 40,105,473 356 1.68 RARA, TOP2A MO_1031 15 60,715,773 102,389,505 3226 1.66 BCL2A1, BLM, CRTC3, CSK, FANCI, FES, IDH2, IGF1R, IQGAP1, MAP2K1,NRG4, NTRK3, PML, SMAD3, SMAD6 MO_1031 1 204,915,769 205,760,704 151 1.62 ELK4 MO_1031 3 12,810,669 19,295,220 467 1.62 WNT7A, XPC MO_1031 12 1,863,550 3,949,766 224 1.62 FOXM1 MO_1031 20 68,356 62,904,843 4648 1.58 ARFRP1, ASXL1, AURKA, BCL2L1, CEBPB, GNAS, HCK, MAFB, MYBL2,NCCA3, NFATC2, PAK7, PLCG1, PTK6, PTPRT, SRC, SRMS, STK4, TOP1, YWHAB, ZMYND8, ZNF217 MO_1031 7 154,237,588 158,937,252 313 1.57 MNX1, SHH MO_1031 14 22,356,506 22,963,536 83 1.53 MO_1031 3 84,962,992 85,156,657 3 1.49 CADM2 MO_1031 17 25,621,074 25,628,926 3 1.48 MO_1031 16 29,808,376 29,819,978 11 1.47 MO_1031 17 20,639,138 22,023,536 51 −0.07 MO_1031 21 9,825,990 9,826,257 2 −0.02 MO_1031 8 2,796,151 3,611,511 66 0.00 MO_1031 22 39,360,598 39,385,480 6 0.04 MO_1031 14 26,917,625 27,377,958 7 0.11 MO_1031 5 177,186,120 177,302,765 3 0.20 MO_1031 1 211,832,141 211,847,090 6 0.24 MO_1031 10 46,961,903 47,087,312 11 0.27 MO_1031 10 135,077,162 135,123,783 35 0.30 MO_1031 10 133,918,368 135,044,448 183 0.36 MO_1031 11 636,612 1,282,788 251 0.36 MO_1031 2 105,472,458 105,488,778 4 0.39 MO_1031 3 20,218,127 23,312,464 14 0.42 MO_1031 12 132,911,966 133,032,417 5 0.42 MO_1031 11 193,171 534,238 107 0.43 HRAS MO_1031 4 7,533,339 10,118,369 180 0.43 MO_1031 16 82,660,648 90,133,269 754 0.43 FANCA, MC1R MO_1031 8 183,094 2,148,837 11 0.44 MO_1031 4 3,076,537 3,534,082 114 0.47 MO_1031 11 63,276,172 64,836,076 405 0.47 ESRRA, MEN1, VEGFB MO_1031 10 135,125,386 135,381,649 77 0.48 MO_1031 6 31,865,505 31,867,955 3 0.48 MO_1031 5 177,419,839 180,687,459 418 0.50 FLT4, MAML1, NHP2 MO_1031 11 55,433,136 57,480,180 182 0.51 MO_1031 12 100,451,433 100,463,882 4 0.52 MO_1031 10 255,897 9,450,260 491 0.53 GATA3, KLF6 MO_1031 18 71,740,798 78,005,236 223 0.53 MO_1031 11 49,059,002 55,340,015 39 0.53 MO_1031 10 123,658,413 133,795,411 542 0.53 MO_1031 17 6,108 20,492,914 2733 0.53 ALOX12B, AURKB, C17orf39, COPS3, CRK, DVL2, FGF11, FLCN, GPS2, MAP2K4, NCOR1, RABEP1, RPA1, TNK1, TP53, USP6 MO_1031 16 34,257,075 62,055,226 1163 0.54 C16orf57, CYLD, NUP93 MO_1031 11 2,154,292 9,229,136 832 0.54 CDKN1C, IGF2, LMO1, NUP98, RBMXL2, RRM1 MO_1031 6 154,727,562 170,893,472 890 0.55 ARID1B, IGF2R, PARK2, TBP MO_1031 3 37,308,321 66,550,768 3147 0.55 ALAS1, BAP1, CTNNB1, FHIT, MAP4, MST1, MST1R, MYD88, PBRM1, PTPRG, SETD2, WNT5A MO_1031 3 4,817,048 12,791,326 579 0.55 FANCD2, PPARG, RAF1, VHL MO_1031 8 41,166,434 43,212,028 260 0.55 IKBKB, KAT6A MO_1031 17 26,488,181 34,207,360 973 0.55 NF1, RAD51D, RHOT1, SUZ12, TAF15 MO_1031 1 205,859,650 206,331,182 33 0.57 MO_1031 10 48,371,062 74,326,404 1228 0.58 NCOA4, PRF1 MO_1031 9 71,986,384 101,817,485 1617 0.58 FANCC, GALNT12, GNAQ, NTRK2, PTCH1, ROR2, SYK, XPA MO_1031 8 3,855,468 31,497,817 1532 0.58 BLK, FGF17, FGF20, NKX3-1, NRG1, PTK2B, TNKS, WRN MO_1031 11 13,391,238 21,596,574 669 0.58 MO_1031 1 211,847,711 233,105,699 1448 0.59 H3F3A, PSEN2, WNT3A, WNT9A MO_1031 10 13,629,072 17,127,612 236 0.59 MO_1031 11 93,065,442 93,148,321 14 0.59 MO_1031 11 93,428,784 94,597,928 135 0.59 MRE11A MO_1031 10 104,809,500 122,688,216 1135 0.59 SHOC2, TCF7L2 MO_1031 11 99,429,012 134,257,653 2837 0.59 ATM, BIRC2, BIRC3, CBL, CHEK1, DDX6, ETS1, FLI1, GUCY1A2, HMBS, MLL, PDGFD, POU2AF1, SDHD, UBE4A, YAP1, ZBTB16 MO_1031 15 29,346,459 60,690,024 2861 0.59 BUB1B, FGF7, LTK, NOP10, RAD51, SPRED1, TYRO3 MO_1031 5 138,611,754 138,860,952 58 0.59 MO_1031 14 56,585,346 82,000,118 1909 0.59 C14orf133, ESR2, FOS, HIF1A, HIF1A, MAX, MLH3, NUMB, PGF, PSEN1, TSHR MO_1031 5 135,277,073 136,328,170 48 0.59 SMAD5 MO_1031 10 88,718,542 104,680,474 1742 0.60 BLNK, CHUK, CYP17A1, FAS, FGF8, GOT1, LDB1, NFKB2, PTEN, SUFU, TLX1, TNKS2, WNT8B MO_1031 1 234,350,230 240,656,524 462 0.60 MO_1031 11 77,830,326 78,489,599 57 0.60 GAB2 MO_1031 4 61,788,424 65,275,026 44 0.60 LPHN3 MO_1031 X 2,700,167 102,755,742 3800 0.61 AR, ARAF, ATRX, BCOR, BMX, BTK, CCNB3, DDX3X, ELK1, FAM123B, FANCB, FGF16, FIGF, FOXO4, FOXP3, GATA1, KDM5C, KDM6A, MAGED1, MED12, PIM2, SSX1, SSX2, SSX3, SSX4, TBX22, TFE3, USP9X, WAS, ZRSR2 MO_1031 10 17,702,514 46,222,766 1080 0.61 MLLT10, RET MO_1031 5 125,696,010 134,106,614 636 0.61 ACSL6, IL3, RAD50, TCF7 MO_1031 6 151,144,864 151,939,184 68 0.61 MO_1031 9 3,453,732 26,101,343 768 0.61 CDKN2A, CDKN2B, JAK2, NFIB, PSIP1, PTPRD MO_1031 18 18,539,877 58,309,304 1673 0.61 ASXL3, CDH2, GATA6, MALT1, MBD1, PIK3C3, ROCK1, SMAD2, SMAD4, SMAD7, SS18 MO_1031 3 239,492 4,558,246 119 0.62 CRBN MO_1031 4 165,876,302 190,903,876 826 0.62 VEGFC MO_1031 3 67,546,367 81,810,649 304 0.62 FOXP1, MITF, ROBO2 MO_1031 1 211,526,618 211,751,637 16 0.63 MO_1031 6 37,180,450 124,442,998 4130 0.63 BACH2, BAI3, CCND3, EPHA7, FOXO3, FOXP4, FRK, FYN, PKHD1, PNRC1, PRDM1, PTK7, RAB23, ROS1, TFEB, VEGFA MO_1031 6 142,399,794 145,823,742 193 0.63 PLAGL1 MO_1031 14 20,201,656 20,404,300 15 0.63 MO_1031 9 71,080,062 71,152,243 7 0.64 MO_1031 4 25,758,416 43,032,450 578 0.64 PHOX2B, RBPJ, RHOH MO_1031 3 32,726,898 37,190,419 251 0.64 MLH1 MO_1031 6 126,176,264 137,245,469 685 0.64 MAP3K5, MYB, PTPRK, RSPO3 MO_1031 2 154,334,924 201,305,468 2736 0.64 HNRNPA3, HOXD11, HOXD13, HOXD4, NAB1, NFE2L2, PDK1, PMS1, SF3B1, SP3, STAT1, STAT4 MO_1031 5 54,415,758 122,522,926 2765 0.64 APC, FER, IQGAP2, MAP3K1, PIK3R1 MO_1031 11 81,601,827 89,955,936 333 0.65 PICALM MO_1031 3 19,322,754 20,216,137 64 0.65 MO_1031 4 74,847,007 75,046,416 16 0.66 MO_1031 4 10,446,372 15,560,868 105 0.66 MO_1031 1 85,869,998 93,913,780 539 0.66 GFI1, RBMXL1 MO_1031 14 28,733,801 31,056,040 27 0.66 MO_1031 4 81,256,954 110,650,894 1362 0.66 AFF1, FGF5, LEF1, NFKB1, RAP1GDS1, TET2 MO_1031 14 39,818,203 48,230,312 133 0.67 FANCM MO_1031 4 44,682,652 44,719,222 19 0.68 MO_1031 3 23,364,968 26,751,572 97 0.69 TOP2B MO_1031 22 23,610,702 23,632,514 10 0.69 BCR MO_1031 6 34,741,320 34,840,216 21 0.70 MO_1051 1 152,484,088 152,816,125 19 3.31 MO_1051 11 6,231,424 6,232,842 3 2.92 MO_1051 20 61,438,941 61,468,452 32 2.42 MO_1051 1 248,604,538 249,211,679 25 2.30 MO_1051 X 34,148,550 34,962,044 10 2.14 MO_1051 X 107,404,842 107,936,036 88 2.07 MO_1051 1 152,657,076 227,843,507 6285 2.01 ABL2, CDC73, CKS1B, DDR2, ELF3, ELK4, ETV3, ETV3L, FASLG, H3F3A, HAX1, IKBKE, INSRR, IQGAP3, IRF6, MDM4, NCSTN, NTRK1, PBX1, PBX1, PRRX1, PSEN2, RAB25, SDHC, SHC1 MO_1051 X 31,792,194 32,235,103 8 1.98 MO_1051 15 25,416,022 25,496,149 41 1.95 MO_1051 1 144,013,934 152,081,884 754 1.94 APH1A, ARNT, BCL9, CHD1L, MCL1 MO_1051 12 54,369,140 54,520,236 16 1.93 HOXC11 MO_1051 1 229,407,014 247,611,745 1149 1.91 AKT3, FH MO_1051 17 46,607,082 46,709,920 23 1.89 MO_1051 X 95,940,052 96,639,008 27 1.81 MO_1051 4 53,298 67,754 4 1.74 MO_1051 7 27,140,656 27,282,803 28 1.71 HOXA10, HOXA11, HOXA13, HOXA3, HOXA9 MO_1051 19 35,803,193 36,018,323 39 1.70 CD22 MO_1051 19 10,077,158 10,108,796 30 1.70 MO_1051 19 36,054,320 36,556,852 179 1.65 ETV2, PSENEN MO_1051 19 45,910,365 46,029,258 32 1.69 ERCC1, FOSB MO_1051 1 152,083,634 152,287,808 27 1.54 MO_1051 2 228,135,522 228,163,484 20 1.53 MO_1051 X 106,893,248 107,403,850 45 1.51 MO_1051 2 227,732,024 227,963,521 37 1.49 MO_1051 16 47,462,728 61,687,744 1025 1.47 C16orf57, CYLD, NUP93 MO_1051 X 107,938,154 117,959,778 339 1.45 IRS4, PAK3 MO_1051 20 29,652,166 59,197,288 2647 1.43 ASXL1, AURKA, BCL2L1, CEBPB, GNAS, HCK, MAFB, MYBL2, NCOA3, NFATC2, PLCG1, PTPRT, SRC, STK4, TOP1, YWHAB, ZMYNDA8, ZNF217 MO_1051 1 40,756,525 40,947,550 42 1.42 MO_1051 20 61,470,000 62,904,843 331 1.42 ARFRP1, PTK6, SRMS MO_1051 X 17,095,401 18,606,234 62 1.42 MO_1051 14 106,303,455 107,283,120 80 1.42 MO_1051 4 74,286,864 75,719,594 90 1.41 AREG, BTC, EPGN, EREG MO_1051 X 31,462,736 31,747,833 10 1.41 MO_1051 X 50,147,176 53,560,271 109 1.41 KDM5C, MAGED1, SSX2 MO_1051 16 97,456 47,117,398 3513 1.40 ABCC1, AXIN1, C

TA, CREBBP, ERCC4, FUS, GRIN2A, MKL2, MLST8, MYH11, PALB2, PDPK1, PRSS8, SOCS1, TNFRSF17, TSC2, ZNF668 MO_1051 7 158,055,758 158,119,500 5 −0.34 MO_1051 12 50,271,607 50,273,606 3 −0.33 MO_1051 12 132,911,966 133,032,417 5 −0.30 MO_1051 6 169,114,856 169,115,787 3 −0.18 MO_1051 4 88,535,422 88,537,643 3 −0.16 MO_1051 9 96,424,692 96,425,932 3 −0.11 MO_1051 7 5,632,990 5,643,110 3 −0.10 MO_1051 7 141,919,835 141,920,772 3 −0.10 MO_1051 19 2,542,606 2,576,124 6 −0.03 MO_1051 17 11,145,036 11,999,005 89 −0.02 MAP2K4 MO_1051 9 139,740,311 139,741,391 4 −0.01 MO_1051 10 134,229,031 134,243,972 5 0.05 MO_1051 21 9,825,990 10,793,947 7 0.11 MO_1051 20 50,225,067 59,793,635 6 0.20 MO_1051 4 30,279,568 31,116,369 12 0.23 MO_1051 11 1,092,230 1,101,070 13 0.26 MO_1051 9 125,239,660 125,487,221 15 0.29 MO_1051 4 25,417,181 25,831,748 34 0.31 MO_1051 9 139,399,337 139,438,456 22 0.33 NOTCH1 MO_1051 7 100,634,044 100,686,182 26 0.36 MO_1051 11 122,859,980 124,489,589 140 0.36 MO_1051 5 140,167,837 140,263,912 57 0.37 MO_1051 22 17,058,814 22,673,386 650 0.41 CRKL MO_1051 6 74,183,252 74,304,854 17 0.42 MO_1051 3 97,711,728 98,251,403 36 0.42 MO_1051 22 39,709,358 51,216,322 1353 0.45 CYP2D6, EP300, MKL1, PIM3, WNT7B MO_1051 9 139,992,316 140,083,683 39 0.46 MO_1051 16 61,689,494 70,884,528 858 0.47 CBFB, CDH1, CDH5, CTCF, NQO1 MO_1051 17 12,011,235 21,207,774 755 0.47 C17orf39, COPS3, FLCN, MAP2K4, NCOR1 MO_1051 4 337,748 25,416,170 1492 0.48 FGFR3, WHSC1 MO_1051 8 183,094 681,251 32 0.48 MO_1051 17 436,106 7,830,984 1445 0.48 CRK, DVL2, FGF11, GPS2, RABEP1, RPA1, TNK1, TP53, USP6 MO_1051 22 23,404,080 39,355,591 1805 0.48 BCR, CHEK2, CSNK1E, EWSR1, MN1, NF2, PATZ1, RAC2, SMARCB1, SOX10, XBP1 MO_1051 22 134,986,740 134,993,900 15 0.48 MO_1051 8 39,521,388 54,730,033 579 0.48 CEBPD, IKBKB, KAT6A, PRKDC MO_1051 17 7,906,986 10,728,695 481 0.49 ALOX12B, AURKB MO_1051 11 5,730,622 6,226,929 35 0.50 MO_1051 16 89,300,336 90,142,217 221 0.51 FANCA, MC1R MO_1051 16 71,209,628 89,294,050 1193 0.53 MAF, PHLPP2, PLCG2, ZFHX3 MO_1051 11 110,306,688 122,653,778 1220 0.53 CBL, DDX6, HMBS, MLL, POU2AF1, SDHD, UBE4A, ZBTB16 MO_1051 12 208,418 18,576,865 1758 0.54 CCND2, CDKN1B, ETV6, FGF23, FGF6, FOXM1, ING4, KDM5A, LRP6, NTF3, PIK3C2G, STYK1, WNT5B, ZNF364 MO_1051 8 1,497,380 38,879,197 2010 0.55 BAG4, BLK, FGF17, FGF20, FGFR1, GPR124, LSM1, NKX3-1, NRG1, PTK2B, TNKS, WHSC1L1, WRN, ZNF703 MO_1051 11 124,493,156 134,257,653 661 0.56 CHEK1, ETS1, FLI1 MO_1051 12 19,282,894 21,168,580 85 0.57 MO_1051 4 31,129,613 69,885,766 1352 0.57 CHIC2, EPHA5, KDR, KIT, LPHN3, PDGFRA, PHOX2B, RHOH, TEC, TXK MO_1051 17 41,957,310 42,636,450 157 0.57 G6PC3 MO_1051 X 63,005,978 79,938,015 771 0.61 AR, ATRX, FAM123B, FGF16, FOXO4, MED12, TBX22 MO_1051 2 170,019,028 170,101,253 41 0.62 MO_1051 X 118,109,145 118,145,782 9 0.62 MO_1051 22 22,781,917 23,230,282 44 0.62 MO_1051 1 120,480,070 142,540,225 24 0.63 NOTCH2 MO_1051 12 22,354,800 23,696,160 49 0.63 MO_1051 7 128,457,794 128,527,239 46 0.64 MO_1051 12 57,543,422 57,604,578 56 0.64 MO_1051 4 25,834,611 30,222,415 79 0.65 RBPJ MO_1051 20 68,356 29,633,982 1441 0.65 PAK7 MO_1051 4 106,369,290 107,158,004 67 0.65 MO_1051 16 47,120,256 47,409,815 19 0.65 MO_1051 X 2,947,315 9,621,620 102 0.66 MO_1051 15 50,450,347 23,686,296 97 0.67 MO_1051 3 96,585,718 97,705,619 67 0.70 EPHA6 MO_1051 4 85,827 331,662 17 0.70 MO_1051 11 4,411,528 5,602,632 88 0.71 MO_1051 19 36,685,981 37,689,941 106 0.71 MO_1051 11 862,652 1,091,424 89 0.71 MO_1051 19 52,497,138 53,716,488 176 0.72 PPP2R1A MO_1051 21 45,736,218 46,311,818 115 0.73 MO_1051 15 25,232,160 25,351,768 30 0.74 MO_1051 17 41,168,284 41,603,952 90 0.74 BRCA1 MO_1069 17 81,006,503 81,083,588 6 4.47 MO_1069 18 641,494 736,954 28 4.38 YES1 MO_1069 17 67,512,994 68,171,885 13 4.32 MO_1069 17 65,528,925 66,453,492 105 3.90 MO_1069 17 63,746,813 65,214,752 91 3.83 MO_1069 17 71,232,438 73,874,342 538 3.70 GRB2 MO_1069 12 8,906,702 8,925,873 2 3.59 MO_1069 17 74,846,540 76,100,688 77 3.36 MO_1069 17 46,154,428 46,928,948 72 3.33 HOXB13 MO_1069 1 211,749,146 211,847,883 10 3.02 MO_1069 18 158,542 633,304 51 2.95 MO_1069 1 248,201,992 248,367,364 9 2.87 MO_1069 18 739,832 1,278,637 14 2.86 YES1 MO_1069 17 48,423,574 48,721,012 126 2.54 MO_1069 17 60,064,432 63,739,228 442 2.43 AXIN2, CD79B MO_1069 17 80,575,285 80,992,948 79 2.40 MO_1069 6 135,778,773 135,839,774 11 2.35 MO_1069 17 65,336,945 65,374,292 11 2.35 MO_1069 17 53,798,298 80,062,226 627 2.09 BRIP1, PPM1D, RAD51C, RNF43, RPS6KB1 MO_1069 2 44,008,719 44,139,663 44 2.05 MO_1069 17 76,104,556 80,574,524 916 1.98 AATK, BIRC5, RNF213, RPTOR, TMC6, TMC8 MO_1069 17 73,887,101 74,774,345 247 1.97 SRSF2 MO_1069 11 65,960,946 67,290,032 367 1.96 AIP, RBM14 MO_1069 17 48,733,210 51,901,464 138 1.93 MO_1069 17 46,929,932 48,356,715 222 1.93 PHB, SPOP MO_1069 17 66,511,554 67,178,942 147 1.92 PRKAR1A MO_1069 17 69,334,538 71,228,340 34 1.91 MO_1069 11 67,352,142 134,257,653 4523 1.90 ATM, BIRC2, BIRC3, C11orf30, CBL, CCND1, CHEK1, DDX6, ETS1, FADD, FGF19, FGF3, FGF4, FLI1, GAB2, GUCY1A2, HMBS, LRP5, MAML2, MLL, MRE11A, PAK1, PDGFD, PICALM, POU2AF1, SDHD, UBE4A, WNT11, YAP1, ZBTB16 MO_1069 1 247,737,584 246,185,858 22 1.88 MO_1069 17 43,718,058 46,153,561 271 1.81 WNT3, WNT9B MO_1069 1 248,402,327 249,211,679 37 1.79 MO_1069 2 238,273,091 238,449,050 23 1.73 MO_1069 X 50,055,582 50,167,242 34 1.65 CCNB3 MO_1069 12 5,915,310 6,0626,648 16 1.64 MO_1069 15 101,464,798 101,608,913 34 1.63 MO_1069 20 57,245,562 57,292,974 20 1.59 MO_1069 2 214,727,212 219,146,824 316 1.55 BARD1 MO_1069 2 43,927,208 44,003,978 23 1.55 MO_1069 12 120,111,766 120,173,122 26 1.54 MO_1069 15 72,338,509 91,769,702 1766 1.53 BCL2A1, BLM, CRTC3, CSK, FANCI, FES, IDH2, IQGAP1, NRG4, NTRK3, PML MO_1069 3 195,452,936 195,610,114 40 1.53 TNK2 MO_1069 3 61,734,674 65,433,782 183 1.53 PTPRG MO_1069 3 5,164,069 18,462,351 1018 1.51 FANCD2, PPARG, RAF1, VHL, WNT7A, XPC MO_1069 17 67,181,674 67,501,961 56 1.51 MO_1069 18 70,205,454 78,005,236 238 1.51 MO_1069 3 75,790,546 87,100,805 103 1.51 CADM2, ROBO2 MO_1069 3 97,753,837 98,217,270 20 1.51 MO_1069 19 51,413,897 51,584,944 51 1.50 MO_1069 20 32,441,436 33,012,336 31 1.49 MO_1069 17 42,635,108 42,636,450 3 1.48 MO_1069 2 44,145,334 44,428,753 28 1.48 MO_1069 1 103,480,082 149,899,706 1500 1.48 BCL9, CHD1L, CSF1, FAM46C, NGF, NOTCH2, NRAS, WNT2B MO_1069 7 138,400,628 151,433,128 1172 1.48 BRAF, EPHA1, EPHB6, EZH2, PRSS1, RHEB MO_1069 1 150,912,430 211,654,670 5646 1.47 ABL2, CDC73, CKS1B, DDR2, ELF3, ELK4, ETV3, ETV3L, FASLG, HAX1, IKBKE, INSRR, IQGAP3, IRF6, MDM4, NCSTN, NTRK1, PBX1, PBX1, PRRX1, RAB25, SDHC, SHC1 MO_1069 19 18,218,476 18,391,780 61 1.46 JUND, PIK3R2 MO_1069 8 29,207,626 30,982,114 107 1.46 WRN MO_1069 1 211,923,224 231,155,638 1347 1.46 H3F3A, PSEN2, WNT3A, WNT9A MO_1069 X 48,463,399 48,689,705 44 1.45 GATA1, WAS MO_1069 19 40,514,428 40,589,194 29 1.44 MO_1069 19 54,632,528 54,659,064 13 1.44 MO_1069 16 29,001,065 30,393,825 155 1.44 MO_1069 18 12,008,430 13,105,058 155 1.44 MO_1069 11 50,003,405 56,237,946 67 1.43 MO_1069 1 29,385,200 103,385,894 5195 1.42 ARTN, BCL10, CDKN2C, CMPK1, DPYD, FUBP1, GFI1, JAK1, JUN, LCK, MAST2, MPL, MUTYH, MYCL1, PTCH2, RAD54L, RBMXL1, ROR1, TAL1, TIE1 MO_1069 19 40,095,937 40,225,610 18 1.42 MO_1069 12 63,541,308 101,873,615 1849 1.41 BTG1, DYRK2, ELK3, FRS2, HMGA2, KITLG, MDM2, PTPRR, SPIC, YEATS4 MO_1069 1 231,299,237 247,729,174 983 1.40 AKT3, FH MO_1069 5 137,734,039 138,118,040 51 1.40 CTNNA1, KDM3B MO_1069 16 31,896,454 34,681,986 29 1.40 MO_1069 17 33,611,080 33,638,804 4 0.09 MO_1069 7 100,187,314 100,188,694 4 0.17 MO_1069 17 32,809,035 32,820,286 5 0.18 MO_1069 21 41,140,492 41,462,159 3 0.27 MO_1069 19 11,373,858 11,390,874 8 0.28 MO_1069 9 113,210,718 113,385,698 37 0.39 MO_1069 5 70,841,173 70,844,815 6 0.41 MO_1069 13 109,613,925 109,956,892 79 0.43 MO_1069 5 137,532,229 137,542,289 8 0.44 MO_1069 17 40,089,486 40,164,050 18 0.45 MO_1069 1 39,126,286 39,134,277 3 0.49 MO_1069 1 25,539,630 29,252,385 552 0.51 ARID1A, CD52, FGR, MAP3K6, PDIK1L, RPS6KA1 MO_1069 17 32,822,782 33,606,210 68 0.51 MO_1069 17 33,708,893 36,332,740 564 0.51 ERBB2, LASP1, MLLT6, RARA MO_1069 17 40,192,184 40,923,970 167 0.51 MO_1069 19 10,830,006 11,371,818 157 0.51 SMARCA4 MO_1069 16 51,432,288 69,401,274 1621 0.52 CBFB, CDH1, CDH11, CSNK2A2, HERPUD1, PSKH1 MO_1069 17 6,108 23,543,324 2894 0.52 AURKB, CAMKK1, FLCN, GAS7, GSG2, GUCY2D, MAP2K3, MAP2K4, MAPK7, PER1, TP53, ULK2, USP6 MO_1069 17 36,928,482 39,936,174 751 0.52 BRCA1, ETV4, WNK4 MO_1069 19 7,512,372 8,392,876 226 0.52 MAP2K7 MO_1069 19 11,392,694 18,070,508 1424 0.52 BRD4, JAK3, LYL1, MAST1, PKN1, PRKACA, TPM4 MO_1069 3 197,579,348 197,614,259 7 0.54 MO_1069 6 68,655,658 126,361,388 2422 0.54 EPHA7, FRK, FYN, GOPC, MAP3K7, PRDM1, ROS1, TTK MO_1069 9 126,773,579 130,420,973 558 0.54 CDK9 MO_1069 45,065,780 49,742,682 362 0.54 CYLD MO_1069 16 69,767,130 87,910,942 1206 0.54 CBFA2T3, MAF, MLKL MO_1069 1 752,046 25,445,741 3061 0.55 CDA, EPHA2, EPHA8, EPHB2, MTHFR, PAX7, PINK1, PRDM16, PRKCZ, RPL22, SDHB, TNFRSF14 MO_1069 6 36,128,488 83,053,829 1872 0.55 CCND3, ICK, MAPK13, MAPK14, PIM1, PTK7, STK38, TFEB, TTBK1 MO_1069 9 70,284,154 94,206,698 1056 0.55 DAPK1, GNAQ, NTRK2, PRKACG, ROR2, SYK, TRPM6 MO_1069 9 94,778,540 112,840,718 1124 0.55 FANCC, NR4A3, TAL2, TGFBR1, XPA MO_1069 9 113,388,245 126,671,370 989 0.55 NEK6 MO_1069 17 23,824,874 32,807,220 1065 0.55 NEK8, NF1, SUZ12, TAF15, TAKOK1 MO_1069 2 102,140,611 157,175,420 2049 0.56 ACVR2A, BUB1, ERCC3, MERTK, PAX8, TTL, YSK4 MO_1069 9 130,552,829 139,852,678 1690 0.56 ABL1, BRD3, C9orf96, NOTCH1, NUP214, RALGDS, TSC1 MO_1069 13 18,499,113 109,612,623 3022 0.56 BRCA2, CDK8, CDX2, CSNK1A1L, ERCC5, FLT1, FLT3, LATS2, LCP1, LHFP, NEK5, RB1, STK24 MO_1069 15 37,793,066 37,855,893 9 0.56 MO_1069 22 15,438,814 49,563,186 3901 0.56 ADRBK2, BCR, CHEK2, CSNK1E, CYP2D6, EP300, EWSR1, LIMK2, MAPK1, MAPK11, MAPK12, MKL1, MN1, MYH9, NF2, PDGFB, PIM3, SMARCB1, TSSK2 MO_1069 6 160,872,714 170,731,132 449 0.57 FGFR1OP, MAP3K4, MLLT4, RPS6KA2 MO_1069 19 50,688,434 50,721,098 15 0.57 MO_1069 3 214,492 5,000,018 186 0.59 MO_1069 13 109,958,488 114,108,621 377 0.59 MO_1069 8 144,312,499 146,250,262 372 0.61 ADCK5, MAPK15, NRBP2 MO_1069 16 88,333,032 88,669,718 118 0.62 FANCA MO_1129 11 78,525,452 78,614,830 8 10.71 MO_1129 11 76,507,253 77,734,336 152 10.44 PAK1 MO_1129 16 53,403,481 53,496,546 18 8.99 MO_1129 11 73,063,928 73,179,552 31 8.52 MO_1129 16 46,702,906 46,725,038 15 8.27 MO_1129 11 74,883,581 75,442,324 74 8.26 MO_1129 16 47,005,363 47,294,464 18 8.25 MO_1129 11 70,118,324 70,858,343 99 8.05 MO_1129 11 75,776,855 75,907,581 8 7.45 WNT11 MO_1129 11 78,775,826 79,113,172 3 7.42 MO_1129 11 77,820,528 78,523,328 65 7.34 GAB2 MO_1129 11 77,749,826 77,812,121 6 7.33 MO_1129 11 76,075,526 76,432,738 46 7.20 C11orf30 MO_1129 11 75,917,402 76,072,153 4 5.66 WNT11 MO_1129 11 77,814,044 77,817,892 4 5.36 MO_1129 16 47,345,262 48,643,775 120 4.92 MO_1129 16 49,823,481 50,402,219 76 4.80 MO_1129 16 46,597,978 46,695,978 20 4.79 MO_1129 16 46,726,382 47,001,976 38 4.58 MO_1129 16 52,874,786 53,358,370 42 4.51 MO_1129 16 54,317,524 54,967,290 13 4.35 MO_1129 16 56,672,724 56,839,479 26 4.22 NUP93 MO_1129 11 73,669,488 74,880,866 172 3.98 MO_1129 11 68,705,664 70,052,410 81 3.82 CCND1, FADD, FGF19, FGF3, FGF4 MO_1129 16 33,965,608 34,681,986 19 2.67 MO_1129 16 97,458 29,001,065 2902 2.54 ABCC1, AXIN1, C

TA, CREBBP, ERCC4, GRIN2A, MKL2, MLST8, MYH11, PALB2, PDPK1, SOCS1, TNFRSF17, TSC2 MO_1129 1 145,209,248 147,415,496 171 2.02 BCL9, CHD1L MO_1129 1 150,039,962 249,211,679 8247 2.00 ABL2, AKT3, APH1A, ARNT, CDC73, CKS1B, DDR2, ELF3, ELK4, ETV3, ETV3L, FASLG, FH, H3F3A, HAX1, IKBKE, INSRR, IQGAP3, IRF6, MCL1, MDM4, NCSTN, NTRK1, PBX1, PBX1, PRRX1, PSEN2, RAB25, SDHC, SHC1, WNT3A, WNT9A MO_1129 14 22,749,583 22,961,931 35 1.60 MO_1129 11 61,091,464 68,704,130 1737 1.53 AIP, ESRRA, FOSL1, LRP5, MEN1, RBM14, SDHAF2, VEGFB MO_1129 1 144,864,331 145,115,804 44 1.51 MO_1129 11 30,921,108 46,918,422 805 1.49 CREB3L1, EHF, ELF5, EXT2, LMO2, WT1 MO_1129 5 140,648 180,687,459 8736 1.48 ACSL6, APC, ARHGAP26, CSF1R, CTNNA1, FER, FGF1, FGF10, FGF18, FGFR4, FLT4, GDNF, HBEGF, IL3, IL7R, IQGAP2, ITK, KDM3B, MAML1, MAP3K1, NHP2, NKX2-5, NPM1, NRG2, NSD1, ODZ2, PDGFRB, PIK3R1, RAD50, RICTOR, SKP2, SMAD5, TCF7, TERT, TLX3, UBE2D2, WNT8A MO_1129 16 29,141,009 33,953,903 503 1.47 FUS, PRSS8, ZNF668 MO_1129 X 2,700,167 94,318,128 3523 1.47 AR, ARAF, ATRX, BCOR, BMX, CCNB3, DDX3X, ELK1, FAM123B, FANCB, FGF16, FIGF, FOXO4, FOXP3, GATA1, KDM5C, KDM6A, MAGED1, MED12, PIM2, SSX1, SSX2, SSX3, SSX4, TBX22, TFE3, USP9X, WAS, ZRSR2 MO_1129 16 70,883,704 71,127,808 66 1.44 MO_1129 11 48,373,888 50,003,636 30 1.40 MO_1129 11 75,480,074 75,727,920 20 0.44 MO_1129 11 81,601,827 134,257,653 3268 0.44 ATM, BIRC2, BIRC3, CBL, CHEK1, DDX6, ETS1, FLI1, GUCY1A2, HMBS, MAML2, MLL, MRE11A, PDGFD, PICALM, POU2AF1, SDHD, UBE4A, YAP1, ZBTB16 MO_1129 X 95,904,052 154,774,783 2605 0.45 BTK, CUL4B, DKC1, ELF4, FGF13, GPC3, IRS4, MAMLD1, MTCP1, PAK3, PHF6, RBMX, SH2D1A, STAG2 MO_1129 22 17,058,814 51,219,026 3934 0.45 BCR, CHEK2, CRKL, CSNK1E, CYP2D6, EP300, EWSR1, MKL1, MN1, NF2, PATZ1, PDGFB, PIM3, RAC2, SMARCB1, SOX10, WNT7B, XBP1 MO_1129 11 50,003,984 61,090,461 587 0.45 MO_1129 11 71,139,834 73,057,972 257 0.46 MO_1129 11 73,357,684 73,662,078 40 0.46 MO_1167 19 281,501 375,803 27 2.42 MO_1167 7 95,906,650 95,926,311 2 2.38 MO_1167 12 34,179,755 40,265,674 91 1.98 MO_1167 2 61,436,070 61,449,714 6 1.83 MO_1167 16 47,622,910 48,643,775 99 1.82 MO_1167 14 50,081,150 51,132,300 195 1.79 MO_1167 17 26,206,406 81,083,588 7129 1.75 AATK, AXIN2, BIRC5, BRCA1, BRIP1, CD79B, CDC6, CDK12, ERBB2, ETV4, G6PC3, GRB2, GRB7, HLF, HOXB13, NF1, PHB, PPM1D, PRKAR1A, RAD51C, RAD51D, RARA, RHOT1, RNF213, RNF43, RPS6KB1, RPTOR, SPOP, SRSF2, STARD3, STAT3, STAT5A, STAT5B, SUZ12, TAF15, TMC6, TMC8, TOP2A, WNT3, WNT9B MO_1167 8 67,356,790 69,699,728 230 1.74 MYBL1, PREX2 MO_1167 20 17,585,297 17,716,465 26 1.65 MO_1167 20 22,563,126 62,904,843 3391 1.62 ARFRP1, ASXL1, AURKA, BCL2L1, CEBPB, GNAS, HCK, MAFB, MYBL2, NCOA3, NFATC2, PLCG1, PTK6, PTPRT, SRC, SRMS, STK4, TOP1, YWHAB, ZMYND8, ZNF217 MO_1167 2 95,537,503 103,380,773 809 1.44 AFF3, TMEM127, ZAP70 MO_1167 2 239,974,737 242,964,616 471 1.39 MO_1167 12 25,031,453 34,179,497 529 1.36 KRAS MO_1167 9 38,573,205 38,596,389 2 −0.11 MO_1185 1 196,748,491 196,799,835 7 3.41 MO_1185 7 95,951,322 100,320,578 611 2.68 ARPC1A, LMTK2, SHFM1, SMURF1, TRRAP MO_1185 7 63,506,056 95,864,204 1523 2.66 ABCB1, AKAP9, CDK6, GRM3, HGF, MAGI2, SAMD9, SBDS, TYW1 MO_1185 1 248,802,276 249,211,679 20 2.65 MO_1185 7 193,482 37,072,998 2058 2.57 CARD11, ETV1, FKBP9, HOXA10, HOXA11, HOXA13, HOXA13, HOXA9, JAZF1, PDGFA, PMS2, RAC1 MO_1185 7 100,344,251 158,937,252 3847 2.57 BRAF, CREB3L2, EPHA1, EPHB4, EPHB6, EZH2, GRM8, MET, MLL3, MNX1, PIK3CG, PRSS1, RHEB, SHH, SMO, WNT16, WNT2 MO_1185 1 145,415,489 151,547,427 614 2.40 APH1A, ARNT, BCL9, CHD1L, MCL1 MO_1185 1 196,857,390 248,685,378 3899, 2.38 AKT3, ELF3, ELK4, FH, H3F3A, IKBKE, IRF6, MDM4, PSEN2, WNT3A, WNT9A MO_1185 1 151,584,804 196,743,924 3920 2.29 ABL2, CDC73, CKS1B, DDR2, ETV3, ETV3L, FASLG, HAX1, INSRR, IQGAP3, NCSTN, NTRK1, PBX1, PBX1, PRRX1, RAB25, SDHC, SHC1 MO_1185 1 1,221,024 1,231,394 10 2.13 MO_1185 16 97,456 34,681,986 3427 1.84 ABCC1, AXIN1, CIITA, CREBBP, ERCC4, FUS, GRIN2A, MKL2, MLST8, MYH11, PALB2, PDPK1, PRSS8, SOCS1, TNFRSF17, TSC2, ZNF668 MO_1185 18 158,542 15,004,215 819 1.80 YES1 MO_1185 1 142,540,225 145,414,742 50 1.77 MO_1185 3 138,724,967 138,739,359 5 1.76 MO_1185 10 225,997 135,381,649 7791 1.65 BLNK, BMPR1A, CHUK, CYP17A1, FAS, FGF8, FGFR2, GATA3, GOT1, KAT6B, KLF6, LDB1, MLLT10, NCOA4, NFKB2, NRG3, PRF1, PTEN, RET, SHOC2, SUFU, TCF7L2, TLX1, TNKS2, WNT8B MO_1185 X 33,148,306 33,357,442 3 −0.73 MO_1185 12 115,109,830 117,537,171 80 −0.71 TBX3 MO_1185 21 9,825,990 9,826,257 2 −0.55 MO_1185 16 55,844,562 55,862,856 8 −0.25 MO_1185 17 7,107,475 7,7,124,954 11 −0.09 MO_1185 20 32,684,636 32,685,368 2 −0.07 MO_1185 X 34,148,030 154,774,783 4899 0.12 AR, ARAF, ATRX, BCOR, BTK, CCNB3, CUL4B, DDX3X, DKC1, ELF4, ELK1, FAM123B, FGF13, FGF16, FOXO4, FOXP3, GATA1, GPC3, IRS4, KDM5C, KDM6A, MAGED1, MAMLD1, MED12, MTCP1, PAK3, PHF6, PIM2, RBMX, SH2D1A, SSX1, SSX2, SSX3, SSX4, STAG2, TBX22, TFE3, USP9X, WAS MO_1185 11 74,700,123 76,261,098 146 0.13 C11orf30, WNT11 MO_1185 16 46,508,278 55,807,285 552 0.13 CYLD MO_1185 17 7,125,469 22,023,536 1678 0.13 ALOX12B, AURKB, C17orf39, CCPS3, DVL2, FGF11, FLCN, GPS2, MAP2K4, NCOR1, TNK1, TP53 MO_1185 1 2,700,257 25,350,002 2584 0.13 CAMTA1, CDC42, EPHA2, EPHA8, EPHB2, KJF1B, MDS2, MTOR, PAX7, PLA2G2A, PRDM16, SDHB, SPEN, WNT4 MO_1185 18 18,539,877 78,005,236 2224 0.13 ASXL3, BCL2, CDH2, CDH20, GATA6, KDSR, MALT1, MBD1, PIK3C3, ROCK1, SMAD2, SMAD4, SMAD7, SS18 MO_1185 16 55,866,960 70,867,000 1447 0.13 C16orf57, CBFB, CDH1, CDH5, CTCF, NQO1, NUP93 MO_1185 X 2,700,167 33,038,217 1236 0.14 BMX, FANCB, FIGF, ZRSR2 MO_1185 16 71,209,626 90,142,217 1419 0.14 FANCA, MAF, MC1R, PHLPP2, FLCG2, ZFHX3 MO_1185 11 59,540,716 64,883,160 1131 0.16 ESRRA, MEN1, SDHAF2, VEGFB MO_1185 17 6,108 7,106,560 1144 0.16 CRK, RABEP1, RPA1, USP6 MO_1185 11 94,603,981 118,247,352 1413 0.39 ATM, BIRC2, BIRC3, GUCY1A2, MAML2, PDGFD, POU2AF1, SDHD, UBE4A, YAP1, ZBTB16 MO_1185 7 44,121,933 44,146,309 4 0.40 MO_1185 3 77,526,710 77,595,553 7 0.40 ROBO2

indicates data missing or illegible when filed

TABLE 5 SAMPLE 5′ hg19 3′ hg19 # Supporting Fusion ID Gene Chr position Gene Chr position Reads Protein MO_1031 CDC123 10 12272994 LOC550112 4 68582640 172 NO MO_1031 SFRP1 8 41161056 ST8SIA6-AS1 10 17441200 435 NO MO_1031 PLA2G12A 4 110650757 COL15A1 9 101822170 76 YES MO_1031 USP6NL 10 11551593 UNC5D 8 35232883 182 NO MO_1031 PPIF 10 81111338 AL359195.1 10 82012039 667 NO MO_1031 RAB10 2 26257603 SPTBN1 2 54849604 24 NO MO_1031 NT5C3L 17 39991321 SPATS2L 2 201324491 21 NO MO_1031 RAB11FIP1 8 37727937 CCDC3 10 13006451 45 NO MO_1031 LRRC56 11 540132 NELL1 11 21197964 7 NO MO_1031 CADM2 3 85851345 CCDC3 10 13021206 8 NO MO_1031 IPO9 1 201817721 PM20D1 1 205814684 13 YES MO_1031 NLK 17 26459834 AC015849.2.1 17 34211385 40 NO MO_1031 STAM 10 17688377 CADM2 3 85288106 72 NO MO_1031 ARSJ(AS) 4 114880675 TBC1D9 4 141622767 130 NO MO_1031 EVI5 1 93029198 PRKACB 1 84596236 15 NO MO_1031 STAM 10 17686377 PROSC 8 37623043 33 NO MO_1031 ADIPOR2 12 1800377 HEBP1 12 13142347 258 NO MO_1031 LRP5 11 68080272 FAT3 11 92430549 11 YES MO_1051 CMAS 12 22199494 PIK3C2G 12 18641380 73 YES MO_1051 TBCK 4 107163626 PPA2 4 106367658 81 YES MO_1051 ITFG1 16 47399692 NETO2 16 47117706 53 NO MO_1051 GPATCH8 17 42512432 MPP2 17 41961522 24 YES MO_1051 FGFR2 10 123243211 AFF3 2 100453985 138 YES MO_1069 ANKRD11 16 89484691 VPS9D1 16 89723229 46 NO MO_1069 ANKRD11 16 89484691 ZNF276 16 89793757 153 NO MO_1069 MLPH 2 238451302 COL6A3(AS) 2 238259785 1476 NO MO_1069 UBN2 7 138936802 TTC26 7 138854034 18 YES MO_1069 HEXDC 17 80394613 OGFOD3(AS) 17 80371025 7 NO MO_1069 TBCD 17 80772809 FOXK2 17 80544938 24 YES MO_1069 CALCOCO2 17 46928989 CEP112(AS) 17 63755705 43 NO MO_1069 CTNNA1 5 138119060 KDM3B 5 137733866 28 NO MO_1069 ITCH 20 32957275 ASIP 20 32848170 6 NO MO_1129 DDB1 11 61091450 PAK1 11 77066886 208 YES MO_1129 VPS35 16 46702841 SLCO2B1 11 74911268 85 YES MO_1129 RBL2 16 53496566 ANKRD26P1(AS) 16 46602603 99 NO MO_1167 PFFKFB3 10 6268327 LOC399715 10 6368508 10 NO MO_1167 STK38L 12 27450642 PPFIBP1 12 27677297 4 NO MO_1167 JMJD1C 10 65140241 REEP3 10 65281497 11 NO MO_1167 SSH2 17 28120954 EFCAB5 17 28257170 3 NO

TABLE 6 AF-4 = AF4 domain C2A = C2 domain CPSF-A = CPSF A subunit domain ENSTL = Endostatin-like domain FH = Forkhead DNA binding domain FHA = Forkhead associated domain GMPK = Guanylate kinase domain GP = G-patch domain HAD = haloacid dehydrogenase HRD = Hpc2-related domain IBN-N = Importin-beta N-terminal domain Ig = Immunoglobulin domain Kazal = Kazal type serine protease inhibitor domain L27 = Lin2/Lin7 domain LamG = Laminin G domain LDL = Low Density Lipoprotein Receptor Class A domain LY = Low-density lipoprotein-receptor YWTD domain M20 Dipept = M20 Dipeptidase domain MFS = Major Facilitator Superfamily domain MMS1-N = methyl methanesulfonate N-terminal NeuA = NeuAc synthetase PBD = p21 binding domain PDZ = PDZ domain PIK3a = PIK3 accessory domain PIK3c = PIK3 catalytic domain PLA2 = phospholipase A2 domain PPase = Pyrophosphatase domain PTKc = Protein Tyrosine kinase catalytic domain PX = phosphoinositide binding domain RabGAP = Rab-GTPase activating domain RHOD = Rhodanese Homology Domain SH3 = Src homology 3 domain SP = Signal peptide STKc = Serine/Threonine kinase catalytic domain TFCD = Tubulin folding cofactor D C-terminal domain TM = Transmembrane domain TPR = Tetratricopeptide repeat domain TSPN = Thrombospondin N-terminal-like domain UBN-AB = Ubinuclein conserved middle domain Zf = Zinc finger domain 14-3-3 = 14-3-3 phosphoserine/threonine-binding domain

TABLE 7 Variants of ESR1. Coding Amino hg19 Somatic Reference Sequence Reference Acid Sample Cancer Coord Reference Variant Transcript Change Protein Change Carcinoma, 152419923 A C NM_000125.3 c.1844A > C NP_000116.2 p.Y537S Invasive Ductal Adenocarcinoma 152419926 A G NM_000125.3 c.1847A > G NP_000116.2 p.D538G Adenocarcinoma 152419920 T A NM_000125.3 c.1841T > A NP_000116.2 p.L536H Adenocarcinoma 152419923 A C NM_000125.3 c.1844A > C NP_000116.2 p.Y537S Carcinoma 152419926 A G NM_000125.3 c.1847A > G NP_000116.2 p.D538G Carcinoma 152419923 A C NM_000125.3 c.1844A > C NP_000116.2 p.Y537S Carcinoma, 152419926 A G NM_000125.3 c.1847A > G NP_000116.2 p.D538G Invasive Ductal

All publications, patents, patent applications and accession numbers mentioned in the above specification are herein incorporated by reference in their entirety. Although the invention has been described in connection with specific embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications and variations of the described compositions and methods of the invention will be apparent to those of ordinary skill in the art and are intended to be within the scope of the following claims. 

We claim:
 1. A method of treating cancer, comprising: a) assaying a sample from a subject diagnosed with cancer for the presence of a mutation in the estrogen receptor (ESR1) gene, wherein said mutation is selected from the group consisting of p.Leu536Gln, p.Tyr537Ser, p.Tyr537Cys, and p.Tyr537Asn; and b) determining a treatment course of action based on the presence of said mutation.
 2. The method of claim 1, further comprising the step of c) administering said treatment when said mutation is present.
 3. The method of claim 1, wherein said treatement is an estrogen receptor antagonist.
 4. The method of claim 1, wherein said estrogen receptor antagonist is tamoxifen or fulvestrant.
 5. The method of claim 1, wherein the sample is selected from the group consisting of tissue, blood, plasma, serum, endometrial cells, and breast cells.
 6. The method of claim 1, wherein said cancer is breast cancer or endometrial cancer.
 7. The method of claim 1, wherein said detecting comprises forming a complex between said ESR1 gene and a nucleic acid primer, probe, or pair of primers that specifically bind to said ESR1 gene.
 8. The method of claim 7, wherein said nucleic acid primer, probe, or pair of primers bind to said mutation in said ESR1 gene but not the wild type gene.
 9. The method of claim 1, wherein said ESR1 gene is assayed from circulating tumor nucleic acid.
 10. A method of montitoring treatment of cancer, comprising: a) administering a cancer therapy to a subject; b) assaying a sample from a subject diagnosed with cancer for the presence of a mutation in the estrogen receptor (ESR1) gene, wherein said mutation is selected from the group consisting of p.Leu536Gln, p.Tyr537Ser, p.Tyr537Cys, and p.Tyr537Asn; and c) determining a treatment course of action based on the presence of said mutation.
 11. The method of claim 10, further comprising the step of c) administering said treatment when said mutations are present.
 12. A complex comprising a nucleic acid encoding a variant estrogen receptor (ESR1) gene, comprising a mutation selected from the group consisting of p.Leu536Gln, p.Tyr537Ser, p.Tyr537Cys, and p.Tyr537Asn and a nucleic acid primer or probe that specifically hybridizes to said variant ESR1 gene but not a wild type ESR1 gene.
 13. The complex of claim 12, wherein said nucleic acid primer or probe is at least 8 nucleic acids in length.
 14. The complex of claim 12, wherein said nucleic acid primer or probe is at least 10 nucleic acids in length.
 15. A kit, comprising: reagents for detecting the presence of one or more variant ESR1 polypeptides or nucleic acids encoding said polypeptides.
 16. The kit of claim 15, wherein said reagents are selected from the group consisting of a nucleic acid primer or probe that specifically hybridizes to said variant ESR1 gene but not a wild type ESR1 gene and an antibody that specifically binds to said ESR1 polypeptide comprising a mutation but not to wild type ESR1.
 17. The kit of claim 15, wherein said nucleic acid primer or probe is at least 8 nucleic acids in length.
 18. The kit of claim 15, wherein said nucleic acid primer or probe is at least 10 nucleic acids in length.
 19. The kit of claim 15, wherein said nucleic acid primer or probe is at least 20 nucleic acids in length. 